Looks like you are running Linux.
I'm not a Java programmer, so I can only report my experiences and observations...
I've never had any problems running the n2t tools on 32-bit Ubuntu Linux, but I haven't worked it very hard. I doubt I've tried any of the Computer tests.
The crash traces all look like drawing problems, two of them with scrolling.
Under Windows XP I've seen strange problems if the HDL contains more parts with UI than are expected. For instance, if there are multiple RAM16Ks in Memory.hdl. (I was experimenting with caching...) The part windows end up in strange places.
There appear to be issues related to threads running on multiple processor cores. I've seen things drawn in the wrong place, which symptomatic of bad/stale pointers, which could easily result in crashes like you are getting. I was able to eliminate this problem by limiting Java to a single core. (IIRC, this was when I was playing with multiple RAMs.)
If you want to, zip up your entire projects/05 directory and send it to me. I'll let you know if I see anything and if I can reproduce the problem on 32-bit Linux or 64-bit Win7. My Dell PC hates 64-bit Ubuntu for some reason. 8-(
--Mark