Despite your cleaning, my first inclination would still be some coating or other.
If you have some more of that suspect blank stock, it might be interesting to do an experiment, take a fresh piece, divide it into three, the first piece is your control don't do anything, the second piece clean in your usual manner, and the third piece sand with some fine grade sand paper (I use 800 to 1000 grit myself), dump all three in etchant and see how they go, no need for artwork, just to find out if there is some unseen inhibiting coating that your cleaning hasn't removed successfully. For bonus points, do the same with a piece of stock which has etched well for you in the past to remove problems like unexpected H2O2 degradation.
As for drilling, I always just use HSS bits, they work fine for the odd board that a hobbiest does, chuck em out after 50 - 100 holes. Also as previously mentioned, etch the centers of the holes away rather than punch them.