@VirtualBrown Looking back at the M122 report you posted, I see:
=== DDARing 0 === Scheduled moves 2526188, completed 2526188, hiccups 0, stepErrors 0, LaErrors 0, Underruns [302, 1, 1064], CDDA state -1It's the Underruns [302, 1, 1064] that will have been causing pauses.
The first underrun number is the number of 'lookahead' underruns, i.e. there were not enough spaces available in the move queue to do full lookahead. This type of underrun causes movement to be slower when there are very many short decelerating segments in succession. This should not cause a pause/stutter.
The second figure is the number of 'prepare' underruns. This indicates that the step interrupt service routine wanted another move, but although there was one it had not been prepared for execution. If the SD card was struggling to supply the next move, the processor may not have had time to prepare it for when it was needed. This may cause a stutter.
The third figure is the number of "no move" underruns. This indicates that the step interrupt routine wanted another move but none was available. If the SD card couldn't supply the next move in time to even be prepared, this will cause a stutter.
To check everything is okay now, start a print job, send M122. This will clear any existing errors. At the end of the job, send M122 again and see if it reports any of the above errors.
Probably just reformatting your original card would have cured it; I expect it was just running out of space, and causing files to be fragmented and taking longer to read.
Ian