The Cool Solutions article at http://www.novell.com/coolsolutions/tip/19465.html describes a way to avoid port conflicts with POA files. Here's an additional workaround that you can try ...
You can also edit the student.poa file and insert the new ports on the appropriate lines of the file. Once the POA starts up the first time, it will also read this information from the DS and store it inside the DB file.
To be neat and tidy, allow the POA sufficient time to retrieve updates - the amount of time it takes to remark out the port lines in the .POA file should be enough for this. Then shut down the POA and restart it without the ports specified in the POA file, and life will be good.
The bottom line here is that the GroupWise system already knows what it needs; it's just that the Post Office (POA) needs to get the update information. By performing a rebuild or forcing a port via the POA file, you are doing just that.
The POA file will be (by default) in sys:system on NetWare, in /opt/novell/groupwise/agents/bin/share on Linux and c:\grpwise on Windows.
Disclaimer: As with everything else at Cool Solutions, this content is definitely not supported by Novell (so don't even think of calling Support if you try something and it blows up).
It was contributed by a community member and is published "as is." It seems to have worked for at least one person, and might work for you. But please be sure to test, test, test before you do anything drastic with it.