Hello Nick,
It sounds like your user tuning settings aren't working properly after the track is played or paused. I would use the following article to help troubleshoot the issue, starting at step 3 and working your way down as needed:
Logic Pro X: Troubleshooting basics
http://support.apple.com/kb/HT200260
Start with these three steps, and work your way down the article as needed.
- Ensure Logic Pro X is up to date
Installing the latest update ensures that your software has the latest improvements and enhancements.
Choose Apple () menu > Software Update and make sure that you have the most recent update for Logic Pro X.
You can also download and install updates from the Mac App Store. See Mac App Store: Update OS X and apps for more information.
- Check third-party compatibility
If you're using a third-party audio interface, MIDI interface, storage system, control surface, or plug-ins, check the support area on the manufacturer's website to be sure that you're using the latest version of the relevant driver or other software for your product. For information on troubleshooting possible issues with Audio Unit plug-ins, click here.
- Test with no audio driver
You can isolate issues with audio devices by starting Logic Pro X with no audio driver. Press and hold the Control key immediately after Logic Pro X starts to open. A dialog asking whether you wish to launch audio drivers will appear. Click "No" and see if Logic Pro X starts up normally. If Logic Pro X launches with no audio driver, check with the audio device manufacture for an updated driver. There could also be an issue with an Audio Unit plug-in. For more information see Logic Pro, Logic Express, MainStage: Disable or remove Audio Unit plug-ins to troubleshoot issues.
Thank you for using Apple Support Communities.
All the best,
Sterling