This is so interesting, I have this issue with bedtools, and I spent hours trying to figure out the all the mismatches. Thank you for the tips.
1/ Your bedtools intersect returned zero results. You stared at the screen for 20 minutes.
The BED file looked fine. The command was correct. Everything should have worked.
I've debugged this exact problem hundreds of times. It's almost always one of these 4 traps: