To answer the questions in item 1:
It is highly unlikely that those loop times were choosen based on anything other than personal preference. Think about it, how could they trim those values to make things match when they don't know how fast your computer is, how much latency there in in Windows, or what else your system is doing? I have several loops in my current project that all run with 100-125 msec delays. Why? Because that's what I always use and it works well to prevent a loop from monopolizing LV's execution time (which is why the delays are there in the first place).
To address the broader question of why the overall problem exists, my guess is that you have a race condition either in the code or your test system. Perhaps also an instrument isn'
t getting all the settling time it needs. Start by looking at the specific test steps that fail. If running the test VI in single step mode or with execution highlighting turned on causes the test to work when it normally doesn't, you have a timing problem.
Sorry this is rather general, but without knowing the specifics of the test and the instrumentation you're using all I provide are hints as to what the problem might be.
Mike...
PS, If TestStand really runs your code that much slower than LabVIEW, I think I'd be asking myself whether TestStand is really earning it's keep... But that's just me...