I seem to be having the same sort of problem with VS 2008 Pro on Server 2003 with Office 2007 and WSS 3.0.  And I've tried VS2008 Pro on Vista Business with Office 2007.

I have noticed that that if I drag a control from the toolbox onto the design surface and only edit it in the properties pane it is visible and stays visible.  If I edit the source in any way the control will disappear even after syncing.  If I drag a control into the source view it is never visible whatever I do.  The controls all appear fine if the code is built and run.

I tried everything short of uninstalling and reinstalling VS (not that this seems to be a reliable fix) and nothig is helping.  Any news on a proper fix for this bug?