Snipey, it doesn't sound like you're "flushing out" any calories. Nothing in what you have written suggests any sort of absorption issues. You were maintaining weight on a diet well within the maintenance range. I don't think forcing calories will bulk you up, but patience and persistence at the gym might well do the trick, and your increased capacity is evidence of progress. As your muscle mass slowly increases, your appetite is likely to adjust appropriately. Your diet will matter, of course, but I'm not a big fan of extreme dietary measures. In particular, the fat in all that milk could easily slow digestion and reduce your appetite. Adding some lean protein might be a bit more effective (and natural), though for starters I'd stay away from the powders (just my opinion). At 110 pounds you don't need very many additional calories to add weight.
I suspect everything is fine, but have you had any blood testing to make sure all is well?