I’ve set some custom kb shortcuts for render track, selection, etc. to sample (to match with the same modifiers for F1/F2/F3…/F11/F12)
I used to always select a empty instrument before pressing the render keybind, and I still do but since I turned on the “Auto Capture Instrument From Pattern” it behaves differently. In some way it will render everything correctly but then still place the render over the auto-captured instrument when finalizing render drops the playhead in another pattern.
The Auto-Capture option also conflicts with Overtune. Since Overtune is not programmed very efficiently, it can take some time to render. So sometimes I want to create a new Overtune instr but I’ll have to be careful and either unset “auto capture”, unfollow playhead, or take the cursor to a new track. Or it would just erase the instrument that’s used in the current note-column.
Are you sure you don’t have any particular tool installed that is messing with your pattern contents when the auto-capture instrument is turned on?
That behavior you describe is something i can’t reproduce. I can’t tell for Overtune since i don’t have it, nevertheless, the auto-capture instrument option should not affect content or instrument behavior.