[palosanto]

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2.- I can't get rid of the layers window. I accessed it once and closed it but it keeps appearing every time I enter annotation mode even though I close it every time ...
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I noticed the same thing yesterday. Did a little testing and I think I can reproduce it now. Fully close MSP, launch it again and open a song. Enter annotation mode. Layers menu doesn't pop up. Open and close the layers menu. Close the song. Now, any time you open a song, the layers menu will keep popping up in annotation mode. Only solution I've found is to fully restart MSP again.

That's exactly it.  Same thing here.