The way it normally works is that a program will open a file and mark it's status to show what other programs are allowed to do with it (i.e. if you are actively editing a file, it will be marked read-only). When the program is through with the file, it returns the status to normal to allow other programs to use it.
Sometimes a program is unable to return a file's status to normal. A corrupt folder is one of those things that can cause this. You have to determine if Extension Manager is in error thinking the files are in use, or the files are marked incorrectly. I'm guessing it's a problem with the folder.
You say that you have a lot of extensions. It's possible that is a problem as well. You may have reached a limit. You could try uninstalling one to see if it makes a difference
