Thanks for all the additional options Mitch, I know you hate dealing with Mecanim.
After playing around a bunch I was able to get some very solid results by adding lots more keyframes for enabling and disabling the collider during animations instead of just 1 on and then 1 off. It definitely wasn't a transition issue, so I'm not sure how the inner workings of Mecanim + bounding box follower works but it does seem possible to miss an enable or disable somehow with all the testing I've done.
If my attack anim is 20 frames I basically made 3 frames "enable" the collider and then 3 to disable it to give it a better chance at hitting one of the disables.
The bone collider option could be a last resort but that doesn't easily fix the "sometimes doesn't enable" issue I was seeing.. it would just allow the ability to completely disable them all easily to ensure they don't stick on, but I'm seeing a mix of sometimes not enabling and not disabling.. < 5% of attack animations.
The game currently runs at about 90fps so I can't see it being a frame skip issue.