Can you tell me if you have Automatic Mass Storage Mode enabled?
This can be determined in Settings -> Media Card -> Auto Enable Mass Storage Mode When Connected
If this is set to 'Yes', that would cause this issue. The problem is that only one device can see the media card at a time (either the blackberry or your desktop). So when mass storage mode kicks on, the blackberry can no longer read the media card (which it's using the play the podcast), and it's freaking out. (It probably shouldn't freak out, which I'll fix later, but it will have to stop the player at a minimum).
Podtrapper detects mass storage mode and disables downloading already, so I'll add code to stop the player as well without dieing. Until then, though, the easy solution is to switch that setting to 'Prompt' for mass storage mode, that way if you don't need it you can let Podtrapper keep operating.
Hope this helps, let me know if I got incoherent anywhere