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Just got confirmation from Helios that they could reproduce it, and it should be fixed in the next release. Yay!

Having them as normal document windows sounds like a good workaround.
But I do prefer them at the bottom of the screen, so I can see both the compile errors and my code at the same time.

Hopefully someone from Helios is able to reproduce and fix the problem for the next release.

Same problem happens here as well (using 5.4.2).

Normally my Tool and Search output windows are minimized at the bottom. But often when starting TP, or switching to another workspace, they've changed to 'normal documents', and their tickboxes in the Preferences window are unticked.

In some cases ...