I'm not sure exactly how it happens prolly to do with something like a shifting memory address for values but the 9999 entry against things which aren't souls will occur if you leave the cheat for 9999999 souls enabled. I found it worked best if I just hit the num1 and cop the souls increase which stays after you disable that cheat, and then hit num1 again to disable the cheat.
There are some anti cheat traps in the game which are subtle and even that wasn't perfect. I have taken to editing the save game money values to change the number of souls without crashing dramas, rather than using the cheat. The "continue" default save file is save00.blk The other two cheats don't appear to cause any drama although I am careful to disable them between levels.