Have the same issue, running 10.1U on an old 3DSXL. But I can still dump and inject saves just fine (when Tubehax decides to actually load)
This seems to only happen to me for ACNL, so perhaps it's a digital games thing or maybe it's just ACNL or maybe it's a combination of things I don't understand.
Solution:
- Open save manager, move left to ACNL, press 'A' to select.. When the screen glitches out, wait until all the glitchy pixels on screen have stopped moving, then press 'A' to dump. You will see the glitchy pixels move for a bit then stop. When they stop, press X to exit. The screen will go all "Super Mario Crackmania' on the top screen. Shut off the 3DS. Your files are now dumped. Same thing to inject a save, but press 'B' instead of 'A'.
Don't do anything until all pixels have stopped changing,