Hi Ian,
It's possible an .ini flag is effecting this behavior, however there are no specific settings that ignore pedal on stop. I suspect you are getting stuck notes on stop. Try raising the playback buffers to 500 or more in Preferences - MIDI - Playback and recording.
If the problem persists please answer the following:
1. What device or plugin are you sending MIDI to.
2. Did this always occur or is it new to this new setup?
3. Is this during playback, recording or both?
4. Is this specific to a project or can you make this occur in any project?