Some time ago I run into similar problem, but I was not able to reproduce it... until now The troubles are caused by the design flaw in theide. The syncing options don't show up when at least one of the nests is not svn working copy.
I enclose the patched files form uppsrc/ide, you can try to recompile theide and test it. If Mirek agrees, I'll commit the changes ASAP.
Best regards,
Honza
This fix is incorrect, reverted.
The problem is that it now lists some folders multiple times.