Is Netbeans not showing the version control options correctly for some of your directories? Check whether you have accidentally left .svn directories. All source control system directories are hidden by default in Netbeans, which makes spotting this a bit tricky.
Check for whether there is a another repo, e.g. a .svn directory somewhere in your path. Netbeans seems to allow “stacking” source control systems, and will unsuccessfully try to load this versioning data instead of whatever you are using in your repository. This means that you won’t get those pretty markers for modified lines and won’t be able to view history for those files or perform a diff from the Netbeans GUI.
See ~/.netbeans/$version/var/log/messages.log for debugging information. Look for messages related to source control loading failures.
Get rid of the extra directories (e.g. .svn in each directory) in your repo, and delete ~/.netbeans/$version/var/cache/svncache to avoid conflicts with cached incorrect versioning data.