I recommend to move your templates and locallang files (and TS and all the basic stuff) to an extension. There is currently an unresolved (status under review) bug, regarding your problem. You can read more here and here. So if you dont have good reason to keep everything in fileadmin, going to an extension is my advice, since its considered to be better practice anyway.
If you have to keep everything in fileadmin switch back to xml until the issue is fixed, wich hopefully will be the case in 6.2 ...
I'm sorry to cant be of better help.