Another user reported this issue some time ago and I developed a fix he confirmed working. I have had no luck reproducing the error (that seems to be happening with other tools too, not just with the merge tool), despite testing in the same reported Windows 10 version, so the fix is based in debug data he helped with. If you are a licensed user, and want to test it, contact me on the support email address.
The fix will be included in the next release. Thanks for reporting.