Merge branch to the head in CVS problem

Question

Hi everyone!

I understand that CVS is obsolete system in out time but my company use it. Problem is the next. As usual when developing starts we create branch from head and start work. Some times later we re-base branch with head and merge head with branch. It is ok. But every next typically operations are with problem. Many-many files are marked as changed, but in fact files hasn't any changes! . And these files aren't become white they red. It's a problem, because we need to review all of it to be sure that file modified.
To re-base branch with head we have do (using WinCVS):

1.Click Update.. on some branch;
2.Check Create missing directories;
3.Check Get the clean copy;
4.Check Update using last check in time;
5.Select Revision to update;
6.Select Merge type.

Any ideas why this can happen?

Thanks.