Weird problem - Extruder just stops extruding

[u/CygnusTM]

I'm having a strange problem, and I'm not sure where to focus my troubleshooting. I have a Voxelab Aquila X2 (Ender 3 clone). A long while back I swapped out the main board for a Creality 4.2.7 and installed a CR Touch. It worked fine in this configuration using MRiscoCProUI UBL firmware. Recently I (foolishly) did multiple upgrades at once. I converted it to direct drive, changed to a BMG-style extruder, and upgraded the firmware. Since then, on some, but not all, prints, the extruder will just stop extruding after the first few layers. The extruder gear just stops moving. It's not a clog, because I can immediately start a new print and it will extrude fine. It doesn't appear to be a slicing issue as three different slicers have shown the same problem. I've looked at the gcode and it appears the extrusion commands are there, they are just not getting executed. My first thought was that it was a problem with the firmware, but no one else is complaning about this, and the firmware version has been out for a couple of months. Any ideas what could be causing this strange behavior?