My Ibanez s470 has little quarter inch cracks in the finish around the neck. I have heard these are harmless, but my question to you is. Can a harmless finish crack around the base of the neck result from the same error in the guitars setup that cause fret buzz throughout the low E. I have notices that my schector has no cracks in the finish around the neck, but also has no fretbuzz with an action slightly higher. The Ibanez on the other hand has had this fretbuzz since Ive had it for 3 years, and I just noticed these cracks last year so i'm not sure if they've been there as long. The action is set lower then that of the schector and it is floyd rose.
How about posting some pics. Ultra-violet light also helps show finish flaws. If you can, use it to check out the cracks to see how deep they are. Is it possible someone knocked your guitar over and didn't tell you?
Moving on.....
i doubt that the cracks are related to fret buzz. try raising the action a bit and see if that fixes the problem
Jackson RR Professional, early 90's japanese model, with EMG's

Digitech GNX3000

Crate GX 212
I noticed the left side of my trem was set lower then the right making the low strings lower then the high ones. But my next quest is if my strings are rattleing around the trem system or something does it mean they are going bad??? It is my G string when plucked hard it rattles and ones I adjusted my trem my low E stopped buzzing but is rattleing like the G. The strings have been on for a while now.