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Temporarily, when I will be able to figure out w/Wingware Support why this issue happens and is not that easily reproducible (reboot of PC can make it disappear, with proper PEP8 settings in Block Comment Style & Auto-formatter, only to re-appear randomly) I'll provide small workaround :)

comment-toggle works also for block selection, so if you have issues with comment-block-toggle, you can try comment-toggle.

I hope that helps :)