I figured out a workaround. I suspected it might be related to a limiter on my main(post) effect chain, as if it was triggered at the beginning of each marker for no reason. No idea if that was the cause of the problem, but thinking about it led me to this "solution":
I moved the start marker a couple seconds back and made an export between start/end markers with "import to track" enabled. Then I moved the start marker back where it was, muted all tracks except the mixdown, disabled effects on the main track and made another mixdown, this time with "between each marker" option.
