From your description it's hard to tell what's happening from your description, and there doesn't appear to be any relevant information in the Microsoft Knowledge Base, so while we can't say what the problem is we can rule out some things. Because the VPN is still connected, it's unlikely that your client is experiencing VPN timeouts or negotiation problems. Because the users do have connectivity for a few minutes, you don't have a firewall problem or other difficulty in making a connection to the servers.
To help diagnose the problem, make sure that the ISA logs are enabled (see this Knowledge Base article for help in configuring them) and check them for indications of problems after your client's users lose connectivity. If the logs don't reveal the problem, you will have to use a package capture utility, such as tcpdump or OmniPeek, to see where the packets are being lost.
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