So for some reason when I edit or add a new prefix I have to rebuild the cache to make the edits work.
And you're sure you have the new copy of the admin file for prefixes?? Run the File Verification in the Tools & Maintenance section, does it say any files are changed??
Yes it says allot of files are changed. I also found this to.
<admin directory>/modules/config/thread_prefixes.php Changed
^ can you replace thread_prefixes.php with a fresh one from latest download package for your version of myBB ..
Well the file is now removed from the file verification, is that good? o.o
^ yes. AND you may like to replace all such files except the files manually edited by you ...
If there were lot of files listed as changed then you hadn't uploaded the files properly, lots of things won't work properly.