You didn't mention a make or model of MIDI interface so I'll throw this in just in case.
This is the kind of problem people get when they use some of those cheap USB to MIDI cables off eBay. These units are notorious for choking on large amounts of data at once. They work fine for sending note information back and forth from synth or controller to DAW sequencer but throw a sysex at them and they tend to lose their way a quarter or half way thru a 50K file. I suspect these cables were built without buffers.
Not all of these have this problem but there are so many different brands of them (many clones under different brand names) it is hard to distinguish which are good and which aren't.