When the thing faults, click "go to fault" from the pull down in the top left corner where it says "faulted". It will tell you where and why.
Sounds like you've included some math things that the processor don't like in the new files. But if you click go to faulr, or look at faults under processor status, it'll tell you why it faulted. The thing I see most in my code is "math overflow trap". And the where faulted is at the last rung of file 2. The culprit rung sets the overflow bit, but the processor won't fault till the last rung, if the bit's still set. You could put an unconditional "unlatch" of the bit as the last rung of your program, but that's cheating. Besides if the bit gets set, something's not gonna work right, anyhow.
Another reason could be a negative timer or counter preset.
There's lots of things that will fault the SLC, but it's always programming errors in my case.