Playing with the latest KSP, DR and FAR, I seem to have an issue. Basically even simple designs, with only stock parts, will have temperature issues on re-entry. For example, a MK1 command pod with a 1.25 payload bay below it and then a standard 1.25m heat shield below that, at 120 ablator; or a MK1 lander can / Hitchhiker Storage Container / 2.5m heatshield stack with 120 ablator.
In both cases the ablator never runs out; rather, it seems the temperature transfers through the heatshield towards the part directly behind it (respectively for my two examples, the payload bay and the hitchhiker module) too much; its temperature raises and it ends up exploding (the heat shield doesn't though, although it ends up separated / hitting the ship as a result). This happens both at 120% or 100% reentry temperature settings (the usual KSP setting I mean - I tried both values), and when re-entering from low kerbin orbit (~100/200K) and at all re-entry periapsises I tried: 10K, 20K, 30K, 45K, and anything above gave me an okay aerobraking on the first run and the same issue when I actually re-entered on the second run.
Now here's the weird thing: I can avoid the issue *most* of the time if I "wobble" the re-entering ship. That is, instead of pointing it straight retrograde (the heat shield against the atmosphere), I tend to wobble it all around the retrograde pointer actively during re-entry; this seems to regularly, by small steps, decrease the temperature of the affected part (not the heatshield but the part behind it). If I stay in the same position too long it will increase and eventually explode though.
I've looked at the KSP log file while this was occurring and there were no DeadlyReentry messages being emitted. Any idea what could cause such an issue ?