Troubleshooting.
There isn't a lot that can go wrong., but CVS is a large system and things do go wrong. Since the whole system is based on simple files, most things can be fixed relatively easily.
Here are two that I have run into.
1. Renaming a Java class to properly camel case it. Windows saw this as one and the same file. Linux got confused since it wasn't there, but it was. I deleted the file on the windows box and then ran a cvs remove. When I recreated the file and tried to add it I got an error. When I looked in the repository, there was a directory called Attic that contains removed files. (After all these were the "current files" back in version 1.1 If you ever tried to call up a copy of the program as it was a year ago or revision 1.1, this file would be needed.) I needed to rename the file on the Linux box with the proper camel casing.
2. Eclipse will check sub-folders that have been removed if they were ever moved to the repository. The only way to get rid of this checking is to go into the repository and physically remove the sub-folder and its contents.