Is the issue present only with player pro or even the stock music app?

It is possible that post the update Samsung has made certain changes that makes the HTC device not 100% compatible anymore, though it is also possible they come up with a patch to fix it, but unless the issue is widespread I wouldn't expect that to happen.

 

The function off the HTC headphone buttons looks to have been reassigned on the ics update . They work as volume buttons note only instead of skip. This is across all apps (I use mort music player). However you can presumably still use the double and triple click of the call/play button to skip, so no loss of functionality there.in fact, I think it is an improvement!