What version are you running? Most likely, my advice will end up being "upgrade".
The latest release, Xtraction 2016 (15.2.5863.1325) does not exhibit the problems you mentioned.
Looks like we're on 15.1
That's a shame as we're unlikely to be able to upgrade for a while.
The upgrade from 15.1 to 15.2 takes, maybe, 15-30 seconds, including cycling the application pools and stopping/starting the Xtraction services. You will spend more time submitting the change request than doing the upgrade.
If you need assistance, we can help.