@misfire:
I made a few experiments today using the cb2util 'cheats -d' command, and found that some of the cheats I had entered into CodeBreaker myself came out wrong.
The command I used for the test was similar to "cb2util cheats -d cheats > cheats.txt"
(slightly different as it was part of batch file taking arguments)
Here follows an example of the type of error I got, for a 'Disgaea 1 (UK)' cheat code for getting max game-money at pressing a button combo
I originally entered this cheat as:
Code:
L3+Sq => Max HL
E0027FFD 002599C2
2029E040 4E729FFF
2029E044 00000918
But in the decrypted cheats.txt file this came out as:
Code:
L3+Sq => Max HL
EA46C329 6DDEA2BD
2AE4BBA2 4E729FFF
2AE4B7A2 00000918
So even though cheats for other games in that cheats.txt file did come out using proper 'raw' form, those cheats (like this one) that I had originally entered in proper 'raw' form all came out in the unencrypted but obfuscated CodeBreaker form. But even that is not valid.
At first I thought it might be valid obfuscated code, but when I entered it into normal code converters, they all agreed on spitting out the following 'raw' conversion, which is pure garbage:
Code:
L3+Sq => Max HL
E0C26FEC 154F1E12
20995DD7 4E729FFF
20955DD7 00000918
This is absurdly wrong in several ways, the most obvious one being the claimed size of the conditional clause being C2, meaning 194 code lines to follow... 
Fortunately CodeBreaker uses symmetrical obfuscation, so I was able to get the proper conversion done by configuring the converters to use the badly obfuscated code from my cheats.txt file as if it were raw, and produce new output code in the obfuscated CodeBreaker format, which effectively removed the obfuscation and produced output identical to the topmost of my 'code' sections above.
Conclusion:
Apparently CodeBreaker stores codes in at least three different forms for the 'cheats' file.
One form for fully encrypted codes, another for the merely obfuscated codes, and a third form for genuinely 'raw' codes. But it seems that the current version of your program does not yet account for all these forms, and always attempts to de-obfuscate my codes, even though they are not obfuscated...
I think that only a minor change to the program should be needed to eliminate this problem.
Best regards: dlanor