Good idea, I have this issue with both the Motorola H17 and the Plantronics Voyager Pro.

I cannot think of anything out of the ordinary I might have done to my N900 (as far as installing 3rd party applications) that might have caused this behavior.

I believe part of the issue might be that the handsfree devices I am using both support A2DP, and it appears that A2DP is a higher priority on the N900 than the 3.5mm and internal speakers. I cannot, for instance, play music out of the 3.5mm and have a handsfree device connected over bluetooth. The music automatically routes to the bluetooth device the second it connects to the N900.