Not sure if it's the same cause or not, (and looking at that line, possibly not :) but when I started porting gnugo to Nokia's S60 phone platform I had many problems with stack overflow. Gnugo seems to allocate many large structures on the stack
To get around this I moved all the big stack allocations to be on the heap. You can get the modified code from http://gnugos60.sourceforge.net/ . A diff against gnugo
3.6 source should show which bits I changed for the small stack. Note that this change significantly slows down the game though.
For reference, the Intel / ARM workaround for the gnugo sub-tools was similar to what I did, but it didn't cause me any problems.