B9 Cargo Bays and Reentry

[G'th]

So, I've been working on a shuttle like plane, and naturally the point of such a vehicle is the downmass capability provided by the cargo bay. And to do this, I've been using the B9 HL parts because they look better and give me that classic heat shield under belly.

However, what I've found is that depending on my reentry trajectory (Be it higher, or lower, short or long, etc etc) sometimes what I have in the cargo bay will explode. Thus far I haven't actually brought anything down yet, but my docking and airlock apparatus (built with CX's space station bits, which obviously aren't meant to survive unshielded reentry) is exploding. Now, while I can reenter in such ways that it doesn't explode, it still kind of defeats the point as then I'll be doing extra maneuvers to get into position for the right reentry just to avoid something that shouldn't be happening anyway. And it definitely doesn't make sense seeing as the rest of the vehicle isn't even affected when everything in the cargo bay starts exploding and rattling around. (which is awesome, but still)

So my question is, what is there that I can do to fix this? Once the game loads back up for me I'm going to try unclipping the docking apparatus (I had clipped it into the cockpit for looks, but I think that might be why the cargo bay isn't working, as it not all of the apparatus is actually in the cargo bay) and see if it works better, but if it doesn't, is there something in the cargo bay cfg I can change or fix to make this work?

Some notes:

I am using FAR but not DR or Real Heat. I do realize that B9 isn't fully updated for 1.04, but I also can't imagine that a fix for this would be so involved that I'd be better off waiting for an official update. It seems to just be the HL parts that are problematic, as I made a smaller shuttle type craft using the S2 parts and had even more parts clipped in the S2 cargo bay/cockpit and that craft works perfectly no matter what kind of reentry I do (aside from anything stronger than a Mun reentry anyway).