No didn't touch FF7Config.exe after applying the changes. By FF7Config.cfg I take it you mean the ff7_opengl.cfg? Here it is:
EDIT - Sorry, just changed the numbers to 32767, ran FF7Config.exe and used black_chocobo and it worked. I obviously missed the need to run the config again after adding those lines.
EDIT 2 - Happened again. When it worked I hadn't edited the equipment tab or my level. When I changed my level to 99 and put max exp in, added some nice equipment it did the same thing again. HP at 2466 and MP at 10.
Materia I added:
Ultima Weapon
Final attack + Phoenix, HP absorb + master summon, Master Magic + All, Counter (blue) + Double Slash
Mystile
W-Item, W-Summon, W-Magic, Master Command, MP absorb + Double Slash.
Ribbon
Save is at the first save point in the game if that makes a difference.