With the given example of working with threads, I don't get the feeling that the problem is somehow fundamental to computing. It would involve the somewhat-arbitrary threading interface, with decisions differing based on the API (WinAPI? POSIX? cooperative multithreading?) someone made up, with a set of locking primitives currently in vogue (mutexes? semaphores? lockless? message passing?).
Having done a lot of systems programming, my main complaint is that I'm almost always dealing with other people's models. I might be coming across fundamental problems in algorithms, but those are a tiny part of my work.
