***UPDATE*** Please see my posting on the December 2008 CU - http://blogs.msdn.com/brismith/archive/2008/12/17/project-server-2007-december-2008-cumulative-update-released.aspx. The Project Professional 2007 CU - http://support.microsoft.com/kb/959643 has a fix for this issue!
*** 2nd Update *** But also see http://blogs.msdn.com/brismith/archive/2009/02/11/project-server-2007-check-in-still-pending-even-after-december-cu.aspx
I replied to a comment on this topic – but think it warrants a new posting so I have polished my reply and added some stuff. I am aware customers are still having some issues with check-in pending and I think it may be a timing issue around closing and opening Project. I haven’t been able to repro this so would love to hear some consistent repro steps based on the August Cumulative Update – if anyone out there can make it happen to order.
However, I have some ideas what might lead to the issue. When you close Project we now give a message to ensure any saves that are in progress get a chance to complete. However this only waits for the save from client to the queue to complete - then the "real" save from the queue to the database happens - then any publish and check-in jobs. So the client may be closed when the check-in completes and so doesn't get the message – and will still think the check-in is pending. On opening it takes a little while for the communication to the server and the responses for any updates on pending check-ins etc – and you may see a message Offline changes - and if the user does a File, Open immediately then they may see Check-in pending for a project that is really checked in. This will not get updated while the dialog is open. Either closing the dialog and re-opening - or opening a "pending" project (read only) and then closing should flush things through and get the project available. This is by far the best approach rather than clearing the cache as it does not risk any data loss. The above symptoms may never appear on a very fast network, and may appear more often in a WAN situation where there is high latency between the client and server.
But as I say, I haven’t been able to repro, even from home, where I have to traverse my home wireless network, then another wireless link a few miles across the valley before getting on to a T1 link and the internet. Another few hops and I get to my server. The ping time is a pretty respectable 50ms across 9 hops. Just to add a little load to my server I set all my projects publishing from ProjTool too – but I never see check-in pending. Perhaps I need to be saving a much larger project and have lots of custom fields at the task level? So for any repro I’d also like to know project size, custom fields, network parameters such as a ping and tracert to the server.