Hi Matt,
Sorry for such a slow response. For some reason this post slipped through the listserve cracks and we just noticed it. Hopefully you aren't still dealing with this issue.
If you are, a couple thoughts to get started:
1) Do you actually need to use Trigger? If you are looking for generic digital pulses, I typically just use go_high, go_low commands. The Trigger command is designed to be used for triggering other devices and I'm only used to seeing it used internally by other devices. All that said, it should still work as expected since Trigger is a pretty thin descendent of the typical DigitalOut.
2) When it comes to debugging timings of pulseblasters, you are probably best off opening up the compiled shot file and inspecting the generated instructions. They are a bit hard to read, but they follow the basic structure of the timing instructions detailed in the pulseblaster manual. It's good to make sure the programmed values correspond to what you intended. You can also take those instructions and put them into the pulseblaster interpreter, which can check that programming is happening correctly.
3) When you change the clock_limit, you should also change the clock_resolution correspondingly.
4) My knee-jerk intuition, assuming one of the steps above doesn't reveal anything, is that you are encountering some kind of clock timing limitation, and labscript is modifying durations under the hood to respect those limitations.
-David