Windows desktop application testing - TestComplete unexpectedly hides windows during test execution

We have a JavaFX application using a mix of decorated(with the Windows OS providing the title bar, minimize, maximize, and close buttons) and undecorated (custom) windows. During the execution of the automation script, calling activate() to bring the window to the front results in the undecorated windows being hidden and prevents the continuation of testing. When inspecting the properties in TestComplete, the 'Visible' property for the undecorated windows appears to be updated to false.

The issue only occurs with the decorated panels. So, say if we tested a scenario only with undecorated windows, this issue does not occur. However, that doesn't resolve our issue as we use both.

Also, does TestComplete generate any background runtime logs (not test execution logs) that may give a clue to the problem?

Our tests are failing and we are looking for a path forward. Any suggestions will be keenly appreciated.