I have exactly the same issue! Do you have the system on a RAID or just on one single internal disk?
We have a Lion Server on a Mac Mini, with the system on a Promise RAID.
It worked fine for 3 months. Then suddenly it started to when I restarted the machine, everything seemed fine. For 2 minutes, then whatever application you start hangs up and ballooning forever. SSH works fine, but we really need to get into the GUI.
Strangely enough, all services the Lion Server is providing works fine and our users don't notice anything.
Tried repair permissions, start in safe mode and Disk Warrior. Nothing. Also checked the log for something weid, but nothing.