Cannot Uninstall ISA Server if IIS Has Already Been Removed 
Microsoft Knowledge Base Article: 301347 - When you use the Add/Remove Programs tool to uninstall Internet Security and Acceleration (ISA) Server, the uninstallation may not work, and you may receive the following error message:

Clients That Use an Automatic Configuration Script May Not Work Because of Proxy Authentication 
Microsoft Knowledge Base Article: 305204 - Browser clients that are configured to use the default "Automatic Configuration Script" in ISA Server or "Automatically Detect Settings", may be unable to obtain access to Web sites through the Web Proxy service in ISA Server if it is configured

Error Message: Cache Initialization Failure 
Microsoft Knowledge Base Article: 284550 - After you install Internet Security and Acceleration (ISA) Server, the following errors are logged in the ISA Server Management Console: 

Error Message "Could Not Register Smtpfltr.dll" Occurs When You Attempt to Install ISA Server in an Array 
Microsoft Knowledge Base Article: 284761 - When you attempt to install Internet Security and Acceleration (ISA) Server in an array, you may receive the following error message: ISA could not register Smtpfltr.dll The Installation log reports an "80070002" error code. 

Error Message Occurs When You Install Firewall Client 
Microsoft Knowledge Base Article: 294409 - When you try to install Microsoft Firewall Client, you may receive the following error message: Cannot Run 16-Bit Windows Program. Cannot find file C:\Progra~1\Microsoft Firewall Ient\Internal_setup\Setup_a.exe (or one of its components). Check to ensure the path and the file name are correct and that all required libraries are available.  

Error Message: The Format of the Specified Computer Name Is Invalid 
Microsoft Knowledge Base Article: 291356 - When you run the Internet Security and Acceleration (ISA) Server 2000 Enterprise Initialization tool (Msisaent.exe) to populate the ISA Server 2000 schema in Windows 2000 Active Directory, you may receive the following error message: 

Firewall Client Conflict with Third-Party Layered Service Providers Causes Connectivity Problems Microsoft Knowledge Base Article: 303379 - After you install a third-party program (such as the NewDot and Babylon clients) on a computer that is running the Internet Security and Acceleration (ISA) Server Firewall client software, you may experience problems with network connectivity, slow loading of the operating system and error messages on blue screens or STOP error messages. The same problem may also occur if the ISA Server Firewall client is installed after the third party client or provider. 

Incomplete HTML Pages and Random Authentication Prompts If ISA Server Is Chained to Upstream Proxy 
Microsoft Knowledge Base Article: 297080 - If Internet Security and Acceleration (ISA) Server 2000 is chained to an upstream Web proxy server, you may receive incomplete HTML pages and random authentication prompts in the Web browser.

Multiple Authentication Dialog Boxes Are Displayed When You Use Access Control
Microsoft Knowledge Base Article  Q297324 - When a destination set is configured, the client receives an HTTP 407 error for each domain that is restricted. As a result, the client browser is prompted for authentication. If the destination that is set is restricted to a domain that contains multiple links to other domains, an authentication dialog box appears for each unauthorized link. 

Real Player Cannot Connect to the Internet Through ISA Server
Microsoft Knowledge Base Article  Q288734 - In environments where you are using Microsoft Internet Security and Acceleration (ISA) Server 2000 to protect the network, and you configure it to allow only User ID-based access for outgoing Hypertext Transfer Protocol (HTTP) requests, Real Networks Real Player may not be able to connect to any channels to receive audio or video streams. Real Player attempts to connect but it is unable to and only displays a status of "connecting" in the status bar. You may also see this behavior with any client that does not use Web proxy for all HTTP requests.

SecureNAT and Firewall Clients Are Disconnected from the Network  
Microsoft Knowledge Base Article 316356 - If you are using a Secure Network Address Translation (SecureNAT) client computer or a Firewall client computer with Internet Security and Acceleration (ISA) Server, you may be disconnected from the network. When this behavior occurs, no error messages are logged on the ISA Server computer; however, various network error messages may be logged on the clients depending on the program that you are using. 

Slow Response from Downstream ISA Server Using Web Proxy Chaining 
Microsoft Knowledge Base Article: 292018 - When clients that use a downstream Internet Security and Acceleration (ISA) Server service for Web proxy request a Web site on the Internet, the downstream ISA Server may take a long time to respond. 

Some Server Variables Are Not Fully Implemented in ISA Server  
Microsoft Knowledge Base Article: 301380 - An ISA Server Web filter that is using one or more of the following variables will not work correctly: 

The "Automatically Detect ISA Server" Option in the Firewall Client Is Unavailable 
Microsoft Knowledge Base Article: 284690 - When you install the firewall client on either a Microsoft Windows 95-based or Microsoft Windows NT 4.0-based workstation, you can observe that the... 

The Internet Security and Acceleration Server 2000 Firewall Client Is Not Supported on Internet Security and Acceleration Server 2000  
Microsoft Knowledge Base Article: 304919 - At no time should you install or place the Internet Security and Acceleration Sever (ISA) 2000 Firewall Client on an ISA 2000 server. 

The SecureNAT Clients Cannot Access the Internal Resources That Are Published by Means of ISA Server 
Microsoft Knowledge Base Article: 296674 - The secure network address translation (SecureNAT) computer clients cannot access internal resources that are published by means of Internet Security and Acceleration (ISA) Server. These resources are accessible to clients that use the Internet, but the internal (intranet) clients receive a timeout error message. 

Unable to Control ISA If LAT Configuration Prevents Access to DC 
Microsoft Knowledge Base Article: 282035 - When you use an array-mode installation of an Internet Security and Acceleration Server (ISA) Enterprise Edition-based computer, and you accidentally configure the local address table (LAT) so that only the external interfaces are included, the internal network becomes the external side of ISA. When this occurs, it is impossible for the array to query Active Directory for the array configuration, and the ISA Server Control service (ISACTRL) does not start. The user interface of the local ISA Management Microsoft Management Console (MMC) does not display the current configuration, and you cannot correct the LAT from any array member in this array. 

VPN Clients May Not Work on ISA Server Perimeter Networks 
Microsoft Knowledge Base Article: 303530 - From a client on an Internet Security and Acceleration (ISA) Server perimeter network, you may be unable to create a virtual private networking (VPN) connection to a server on the external network. The connection does not work using either PPTP and L2TP 

VPN Dial-up Connections Are Not Filtered by ISA Server  
Microsoft Knowledge Base Article: 313433 - A virtual private network (VPN) dial-up connection from Internet Security and Acceleration (ISA) Server to a remote network is not filtered. This behavior is by design because ISA Server assumes that dial-up VPN connections from ISA Server 

Web Proxy Service Crashes If URL Requests a Specifically Malformed Argument 
Microsoft Knowledge Base Article: 295279 - When an incoming Web request is made to a computer that is running Internet Security and Acceleration (ISA) Server and is publishing a Web page by using Web Publishing, the Web Proxy service may stop and an access violation may occur. 

Windows 2000 Server Cannot Join Existing ISA Array 
Microsoft Knowledge Base Article: 295654 - When you install a new ISA Server-based computer into an existing ISA Server array, you may receive the following error message: