Perhaps, as Trump's nomination becomes more and more likely, those polled are taking the question more seriously?
Before, some people who may have said "sure, I'd vote for Trump in this hypothetical matchup" are now being faced with the stark reality that it is likely actually going to be Clinton vs. Trump, realizing it's not fun and games anymore, and voting for the adult in the room.
This could even have a positive feedback effect, if the dyed-in-the-wool Hillary haters start abandoning Trump because "he can't beat Hillary".