Hi lzimmerle,
The Method Integration Engine starts automatically with QuickBooks through a certificate installed in your QuickBooks company file. You can check for this in QuickBooks by going to Edit > Preferences > Integrated Applications > Company Preferences. There should be two Method applications listed here: Method Integration Engine for use with QuickBooks and Method Integration Engine Listener. Check the permissions on these to make sure they have full access to your file.
If that doesn't resolve your problem, you can try a full uninstall and reinstall of the Method Integration Engine. We have a Help Center article that explains how to do this here (uninstall) and here (install).
If you're still running into issues, or if you would like assistance with the above recommendations, please don't hesitate to give us a call at 1.888.925.6238 x.2 and we'll be happy to take a look with you.
Hope this helps.
- Justin