Do those patterns play without problem if you are not in the Arranger?
Any scenes, lfos or midi modulating the sample start parameter?

Do you have midi going into OT or only out? Afaik, the Arranger sends song position pointer, not only start/stop messages. Not sure if it also receives song position pointer (it’s been a while since I used the Arranger), but you could simply deactivate send transport under midi → sync to test if that somehow causes a problem.
Of course you don’t have to test this if you don’t have midi going out of OT and back into it.

How exactly is your stuff connected via midi?