Hello 4theturck,
Usually when customers see the cursor flickering and QuickBooks is slowing down, Method is syncing over transactions. This may be that Method has yet to get everything from QuickBooks that it needs. What you can do is find a time where you are not using QuickBooks. Run a full-sync and let it run uninterupted. If you are syncing a lot of transactions on your initial sync, you may have to do a couple of full syncs.
Make sure you keep the transaction history low until every transaction is synced over for the time period. (You can find the option under QuickBooks -> Synchronize). If you change it to 'All' and you have a very large QuickBooks file, the engine will have trouble syncing everything over in one go. It's best to increment the transaction history up slowly and run full syncs at each level.
The Listener is loaded when you shut down and open your QuickBooks file again. If you close and re-open your QuickBooks file, does the Listener Certificate come up? If you have not seen it yet, here are some more detailed initial syncing instructions from our Help Center. Make sure you are logging in as the main admin user when setting up the Listener. After, you can sign into QuickBooks with whatever user you like.
If the problem persists, we can help out on the Method support line. 1-888-925-6238 x2.
Greg