i've ZCS NE 5.0.4 installed on a SLES 10 x86 and have the same problem.
Is not something happening on the client PCs, i can Compact the ZDB in Outlook and it does, but even if the email i actually deleted on the client to save space are synced to the server, i still see the Quota numbers unchanged.
1. original quota 2.5 gb on 3 gb
2. tidy up, deleting and compating in outlook: 2 gb zdb file
3. synced correctly
4. quota on server still 2.5 gb on 3 gb
Any help would be really appreciated.