We too are migrating from BEX to NBU (6.0). I have been able to have both clients running together on Win2k3, NW6.0 and 6.5, and on Solaris platforms.
The Netware TSAs really don't like to have both agents actually passing data at the same time, and gwtsafs will bomb if they do. I just pick my times very carefully for NBU at this transition period. I will adjust the schedule windows after I am completely done with BEX.
There have been some load issues with our AIX servers, so I'm having to do those in a separate operation. I think the clients could co-exist with a more robust evironment.
David