If you have several threads of the same type* you could modify your code to only run one of each type of thread (or perhaps put it in the application's configuration file so you can change it quickly while debugging).
If the application still misbehaves then you know that it's an interaction between the different types of thread that's causing the problem. If it doesn't then it could be that there's some resource you've not thread locked properly (for example).
What I'm trying to say is simplify you application to the point where it's using the minimum number of threads to still be your original design.
* Not the best word to use, but for example if you spawn 10 threads to deal with file i/o only spawn 1.