Quickie: When used to configure NLB for an array, ISA Server 2004 Enterprise Edition enables the NLB parameter UnicastInterHostCommSupport, available in Windows Server 2003 SP1 and later.

This means that all other things being equal (eg, your rule set permitting it), two unicast hosts with NLB enabled should be able to chat using their dedicated IP addresses. Remember, any non-dedicated IP address is assumed to be balanced by NLB, so your mileage will vary*.

I mentioned UnicastInterHostCommSupport before (but not that it was enabled by ISA).