Actually, my friend; that's a negative! Success achieved!
As soon as you said "Patching saves", I thought of the M3Real's GUI and how the GBA mode had 2 boot modes; Patch and Fast load. Looking into the M3 Sakura's OS a little more, I found that if you slide the game to the left, you can get to an options screen that has the option to "Low-Speed Load", which is the same as "Patch-Load" on the M3Real. As soon as I swapped that setting, every game that gave me trouble worked fine.
The only hassle is that you have to set it individually for each game (which entails setting it and then restarting your DS) but it's a small price to pay. Besides, once you set it once it's set for good, so one good 5 min session should have everything you need running. Thanks again for your help, TDM.