Haven't heard about that before. There are three things you can do:
a) Upgrade to R 1.7.0 when it comes out "tomorrow" (for largish
values of tomorrow -- depends on what Martyn's plans are for
Easter...) and see if the problem is still there.
b) Next time it happens, run "top" or "ps" in another terminal, figure
out the process ID (say, 7913) and run strace -p 7913 and tell us what
you see.
c) Make a habit of starting R under the debugger: "R -d gdb", then in
gdb use "run". When the bad thing happens, Ctrl-C will bring you back
to the debugger where you say "bt" which might give us a clue. (If you
need to interrupt R for other reasons, use Ctrl-C and enter "signal
2"). You can also attach gdb to a running R much in the same way as
strace.