kh,
Which version of LabVIEW are you using? Built-in SCC have been rewritten from 6.0 to 6.1 and there are different issues related to each version.
With 6.0 I have encoutered a bug that wrongly checked most of my VIs as "local copy has changed" as soon as they are in memory with panel closed. I worked with NI Support and we found no workaround. Unfortunately, this behavior stayed even when the VIs were upgraded in 6.1 so that my problem was a dead end. I switched with great success to CVS, another source code control software.
I do not use 6.1 but if you do, make a search on NI's site and you'll find hits that address a SCC bug. If I remember correctly, checking out a VI, making a small change and checking it in again often solved the problem.
G
ood luck.