Beans and Boxes Clash and Access Fail

So something strange has happened to me. I had a project where I was using beans and boxes side by side. Don't ask why! I didn't realize at the time that boxes here was somehow merging with bean or at least providing similar functionality? I'm trying to dig through the commit logs and understand whats happening more thoroughly.

Thus my situation is that I've created an entire site with 6 different block types, that all ended up being boxes block types to my surprise (I thought I was building bean block types!)! They show up in the boxes permission list even.

Heres the actual bug report >>> This fluke wouldn't be so much of a problem if it werent for the fact that the boxes per-bundle permissions don't work, thus, no matter what I do, unauthenticated users cannot see these block types. I'm guessing its because the per-bundle permissions are applying to beans and not boxes, thus the access callbacks are misfiring? or something? Any news on this front, any patches that need to be written?

For now, im going to 'rescue' my field collections that are attached to my block types by adding them all to a content type, then im going to uninstall boxes and bean, and see where I can go from there! What would folks who are a part of this melding process recommend I do for handling block types? Should I start with the bean module or what? Stay away from dev versions it seems for now?