Boehm GC CVS now has a patch that will fix this behavior. Compile with threads and -DUSE_GET_STACKBASE_FOR_MAIN. See the following thread for details.
http://comments.gmane.org/gmane.comp.programming.garbage-collection.boehmgc/3788 If Hans Boehm agrees, the behavior will probably become default and no flags will be necessary. At this point it's not necessary to patch Guile, as long as valgrinders are willing to use CVS for now. I think that's for the best, since the solution is pretty hacky.