Unfortunately I have not idea what the problem could be. In principle the trigger should be independent of the sampling speed, since the trigger is only made with a discriminator and a flip-flop. The hardware must be ok since you see the trigger with the oscillocope app. All you can do is to go through the sorce code of the oscilloscope app, especially drsosc/Osic.cpp::ScanBoards(), SetTriggerLevel(), SetTriggerPolariy() etc. to make sure you do the same calls as the oscilloscope app.

Stefan