Since the math stack is now hidden from users, it is something that is managed strictly by instructions and DmD. At the end of each instruction, the stack should be resolved to zero depth. For a user program to bust the stack, it requires that an instruction have a broken pathway...one that is leaving something on the stack rather than fully resolving. That is very bad and really needs to be fixed ASAP.
If you can reduce the failing program to something simple, that is great. If not, it's still great...we'll pick through your full program and figure out what is busting the stack. If you are unwilling to send me your program, still no big deal, I can to send you a special build of the 1.0.9 OS that turns on some stack checking. It will log any failures it observes to some system registers that will tell us which instruction is causing the issue. In fact, that might be the easiest path, since it will allow you to run the program with your I/O. I'll PM you my email address and we can conduct the rest of this via email.