It sounds like a driver/latency issue. When BE locks up like that for me, it usually comes immediately back to life as soon as I unplug the QH. Then I plug it back in and all works fine again. Next time it does this, confirm that simply unplugging the QH fixes the lockup. If it does, then you definitely have a driver and/or latency setting issue.
89 Ranger Supercab, 331 w/GT40p heads, ported Explorer lower, Crane Powermax 2020 cam, 1.6RRs, FMS Explorer (GT40p) headers, Slot Style MAF, aftermarket T5 'Z-Spec', 8.8" rear w/3.27s, Powertrax Locker, Innovate LC-1, GUFB, Moates QuarterHorse tuned using BE&EA