@_@ it seems the debug folder structure was broken by this latest release. Everything is working fine, but when debug_mode=yes the replaced textures that are already on the cache will end up in the tonberry\debug\ directory instead of tonberry\debug\replaced\
It was a simple fix but, again, we'll have to wait until JeMa can get my code and upload a new version.
If you are playing with debug_mode=no then this does not apply to you.
This issue has been resolved. Please use version 2.02 for the best Tonberry experience yet.