There haven't been any changes to how loot is generated that I'm aware of. I'll review it, but I don't see anything obvious that may have creeped in. Randomness is streaky though, so it's difficult to get a picture from a handful of data points. One thing to keep in mind is that the skills are determined independently of the item's rarity, so you should keep track of the total number of inaccurate items, not just the ones that are really high rarity. If you got 50 blues and greens with correct skills and 4 yellows with wrong ones... that's just bad luck.

Anyway, I'll look further for any weirdness that may have creeped in, but there haven't been intentional changes in that system.

(Also important to know: loot-dropped augments do NOT use the same system and are MUCH more likely to be for random skills.)