I have now created a work-around for the malloc/free threading issue which creates an extra thread for the mainloop. The startup thread then simply waits for it to be finished. As such, there is never memory allocated in the "main" thread. At least for me, it works now with mudflap. I am still in doubt if that was the segfault issue (or just a bug in mudflap), but at least we can give it a try.
I will now see that I get some feedback. The next thing is change the packaging back to a single source tarball (by popular request ;)).