Alright, 1.0.5 should relax the Win7+ requirement. It was the MSVC 11 build of Allegro I was using. I linked minisphere against the MSVC 9 libs and K32GetModuleFileNameExA disappeared from Dependency Walker. 
I also fixed the maps in subdirectories issue, but now I'm getting an "invalid base value" error whose cause I can't pin down. It can never be simple, can it...
@Radnen: OOH, I see what you mean about the mappings now. I opened the options file, and saw this line:
keys={"upKey":77,"downKey":79,"leftKey":80,"rightKey":78,"AKey":59,"BKey":55,"XKey":60,"YKey":68,"LKey":72,"RKey":76,"startKey":70,"selectKey":61}
...and suddenly understood jack everything.
See, minisphere uses Allegro's key constants directly, it doesn't remap them. Obviously those values are different than whatever Sphere 1.5 defines them as. I never thought it would be an issue since I expected games to always use the named constants, but didn't account for the possibility of keys being saved out to a file...