not sure if this will solve your problem completely... but you could reset your illustrator preference file. Some times Preference files get corrupt. i just set my keyboard increments to 0.0139 and check it against a box that was 0.0139x0.0139 and it lined up when i moved it.. i really think trashing your prefs should help.. also make sure smart guides and all snapping is off... which i understand you have checked... but if you trash your prefs and restart illustrator snapping will be back on by default.
link below for trashing prefs..
http://www.illustratorhints.com/2010/05/delete-preferences-file/
Good luck... please let me know if this works for you.
