Answer:
Kohana 3.3, they didn't take into account case-sensitivity on folders/files (they capitalized some directories/files) so this is going to drive some folks nuts when they start switching to the new Kohana (just like I did).
I switched back to Kohana 3.2 until this has been fixed.
Thank you very much for taking time in reading my huge post I had about this silly problem, and I hope this answer saves a poor souls life in the future =)