This issue has been reported to us once. The reason for the problem was that the Thunder config file was with some invalid configurations. The problem was resolved after deleting the config file. Please check what is recorded in the Thunder.config and paste it here.
@OC did you figure this out? I get this error sporatically, it'll work for a few saves, then it wont.
The problem is that there's nothing in your face saying the save failed...it's a tiny message in the output window. So you think your template saved, but NOPE
I'm sorry, I just can't remember how I solved the issue, but it has not bothered me since.
I believe I re-created the Thunder theme entirely by copy paste into a new theme, but not sure I remember correctly.