Can you post your Meconfig.db and Wcmdmap.db found in the Multi-Edit\Config folder (e.g. C:\Multi-Edit\Config) and a sample *.db file you’re having problems with.
Was it working in 9.10.03?
Check TOOLS -> CUSTOMIZE -> General (left side) -> FILENAME EXTENSIONS,
look for a DB extension in the list (I don’t have one). If one not found look for DEFAULT, click Edit, and check “Tab settings mode” there. Also check “Indent style” there. It may be set to “Smart” or “Auto”, which means it’ll try and be smart and automatically insert tabs to whatever it thinks is right, which sounds like what you described. You probably want “Indent style” set to Off.
Also check TOOLS -> CUTOMIZE -> Editing (left side) and check “Tab expand”. You’ll want that set to Tabs or you’ll get spaces instead of tab characters.