well s-macd, sorry to hear you're having the same problem, but im glad to hear im not the only one! the problem went back to being very occasional again for me, so i wasn't as incentivised to find a cure.
just happened again yesterday on a 989 frame shot. crashed around 450. switched to another comp and it finished just fine. that's the second time it's happen in the last week or so.
there are only two factors i seem to notice with this:
1) it only happens with large files. 98% of the time this happens it's been with 2k cineons. i think it happened once with some hd files (which i only remember because it destroyed my "only with 2k cineons" theory), but i've never seen it with smaller files.
if the problem is file size related it might not be either or, just much rarer with smaller sizes and thus not encountered as often. also, i primarily work with 2k cineons, so i haven't tested smaller sized files as much.
2) it only happens thru a command line render. i've never had this happen when rendering via the gui (shake viewer).
i use five mostly identically configured dual-core g5s. four are used remotely as part of a render-farm and one is one of my desktop units. i used to get weird stall-outs every now and again with qmaster which i now believe is the result of this problem (one machine would stop causing the render to be incomplete).
i use shell scripts to create quicktimes via the g5s since qmaster can't do quicktimes. i run qmaster when simply processing individual frames to individual frames.
s-macd, have you tried rendering via the gui to see if that solves the problem? since you seem to be able to recreate it more consistently than i.