?> I understand why many do 3-4 day counts( to get a more precise average), but I find separating the mites from the hive junk is almost impossible if the sticky boards are in more than 24 hours.

Are you putting the boards in when you super or doing other manipulations?

Newly added boxes will drop wax and junk, but if the bees have occupied the equipment for a while, there should not be much dropping.  We never found that to be a problem in fall, and we often left them in for a week or more.  We had more problems with the bees propolizing the screens since we tipped the doubles back and slid in a board with a screen on it and the screen often touched the bottom of the frames.

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