Though that obviously shouldn't happen with 1.3.6, why are you trying to use it over the autofacet version in the first place? Especially for a hard-angled ship? I've been assuming you were using the autofacet build since I gave you the link in the other thread. :\
Total smoothing on ships with hard angles and flat surfaces looks bad. Faces that are actually flat get shaded as though they are lumps, and small details get totally wiped out. Total smoothing is meant for organic ships; or at least ships made mostly of curves. If you want to add apparent detail, do it with polys rather than smoothing.
Back on the topic of PCS, it does indeed appear that 1.3.6 has a bug in the converter. I tried using it for conversions, and some of my stuff began getting the same stack overflow errors, even though the exact same files will convert without a twitch in the autofacet build.
Considering that some of the 'stuff' includes the TC-Tri (the Triton converts), Aeolus and Lucifer - all of which work without any trouble at all in-game via the autofacet build, I think it's safe to say something broke between then and now.
The odd thing is, both versions apparently use the same 'COB to POF version' - 1.3.4. :\