Hey Con -
I suspect it is a bacteria problem, not a wild yeast problem. I had been having similar issues. All the beers tasted pretty good going into the kegs, however after some time in the keg (where the beers would usually improve with aging) I began to detect what I would describe as an apple-ish / pear-ish taste as well as more of an alcohol/hot presence. I finally figured out the problem: My (now retired...) old stainless 2 barrel fermenter. (There may be some pics of it in my gallery) It is dish bottomed, and came from the manufacturer with a sanitary 1.5" triclover tube welded to the bottom center (yeast / trub dump / drain). No problems there.
I had a stainless coupling installed on the side of the fermenter, above the trub line, used to transfer the beer into the kegs. Because of the shape and size (6' tall with only a 6-8" lid)of the fermenter, it could only be welded on the OUTSIDE of the fermenter. Therefore leaving a small gap between the coupler and the tank wall on the INSIDE of the fermenter. THAT'S where the problem is.... no amount of cleaning/sanitizing even using a brush on a handle could get all the critters out of that little gap.
It took me forever to figure out where the problem was as I am so anal about sanitation. It finally dawned on me to check that fitting with a flashlight through the lid. Also, it took a number of batches for the issue to begin presenting itself - at least a dozen good batches with that fermenter before each one started getting progressively worse.
I feel your pain, man, as it is EXTREMELY frustrating to go from making great beer to making not great beer....especially when you didn't change anything!
I now ferment 27 gallon batches in (2) modified Sanke half barrel kegs that I am CERTAIN the tri-clover connections welds are sanitary/ground and polished - inside and outside. (no pics yet on my gallery.) Also, I am able to steam sanitize them by placing on a turkey fryer burner with a few gallons of water and boiling the h@ll out of it for 30 mins or so while going about the regular brewing activities, which definitely kills everything as well as eliminates the need for chemical sanitizers.
Also, FWIW, I use a chest freezer for ferm. temp control and have had suckback into the fermenters due to temp changes, but haven't had a problem yet. I can see why you would consider this though...as I have had mold and funky smells in there when I accidentally spilled beer/wort in the freezer or even on the LID of the fermenter! However, knock on wood, no problems from that. It did however make me much more fastidious about wiping down and cleaning both the freezer and the fermenters!
Sorry to be so long winded here. I guess my advice to you is look for somewhere on your equipment that you are not able to be CERTAIN is getting cleaned/sanitized. Good luck and I hope you are able to fix the problem soon.