StaffYou have two variables in play here: a change to TestComplete 12 and a change to .NET 4.6.1.
I've seen a similar problem with TestComplete 11.31 and a change to .NET. Try going back to TestComplete 11.31 and your previous version of .NET. Verify that that problem does not exist. Change .NET and check if the problem appears. (I suspect it will.) Now try TestComplete 12 and check that the problem still appears.
Open a support case. There is a patch (CC-6531) to TestComplete 11.31 that may (or may not) fix the problem but you'll need to investigate this with the support team. Further investigation would then be required for TestComplete 12.
Because Microsoft is Microsoft, I would suspect that the problem resides, not in TestComplete 12 but in the new 4.6.1 CLR. If you recompiled your application with the new .NET and it had previously been 4.5 or 4.0, objects may change in how they are identified.
I agree with what joseph_michaud suggests... roll back both TC and .NET and change one aspect at a time. To check to see if it's TestComplete, try just upgrading TestComplete and keeping .NET as the old version and see if the problem still happens.
