Issues with G.G Series Collection+ saving max stage progress after first game over.

Playing this for All Breaker as the DSiware version seems to lack a stage select and arguably has worse sound design. However after my first game over, the game seems to no longer record my max stage clear; which of course neuters the whole point of a stage select. I can reset this bug by wiping my save file with a fresh all unlocked one (like the one provided on this site), but said fix is only temporary. I'm running off an r4i gold plus with wood akmenu 1.64 on an CFW N3DS, so I can get by with real time saving worst case scenario. Though said saving and loading runs slower than a copy of Pokemon GBC and flickers the level geometry for a few in-game steps; so its really more of a last resort to maintain progress than a reliable save scumming tool.

I'm still a novice to the world of CFW and R4 cards, so perhaps there's an setting or a firmware update I'm still missing. Or my 64GB SanDisk Ultra in the r4 could be to blame, I've recently heard about potential hiccups with cards beyond 32GB. This is really the only place I've seen any significant chatter about this Japanese exclusive, so I'm all ears to any advice at all before I throw in the towel.

Update January 2021: I've got my hands on an actual GG Series Collection cart, and unfortunately was able to reproduce the same issue on a fresh save file. 50% chance of a game over yeeting your max stage counter, making stage select utterly useless. Welp, guess I'm relying on save states then.