I ran my .asm file from my VM translator against the test files in the CPU emulator for StackTest. I got the correct values in my registers, but the output file didn't print the second line of registers and values.
Is there something I am doing in my code that creates this issue?
You'll have a better chance of getting an answer if you provide a way to reproduce the problem. Preferably, this would include a step-by-step explanation of what you do and include a small (if possible) version of the .asm file in question, which still demonstrates the problem.
Incidentally, while you're preparing these, you might actually solve the problem by yourself. This happens quite often as the preparation steps make you formulate the problem clearly and you may see what's wrong. If that happens, it would be nice to write answer here :)