Sounds like Twitter have beefed up their spam protection. Hash tags were being ruined by spammers posting crap and then piggybacking on a hash tag. I'm guessing this is to filter out that noise. Your followers will still see your tweets containing URLs.
There's probably some relationship between age of your account / amount of followers and whether they allow your tweets with a hash tag and a URL get included in the search. I'd bet on the amount of followers being the key here but Twitter are unlikely to advertise this, it would give the spammers something to aim for.