After doing some testing you are right, using cheat codes is broken, I tested v3.336 and cheat codes worked fine, even for Batman Rise Of Sin Tzu all codes I tested worked fine, I'm not sure which revision broke it, would do some more testing once I get some time and more importantly "learn how to download older versions" because I just so happened to have a copy of 3.336 on my other hard drive.
This brings me to another issue, I re-read the first post multiple times and I swear I could not find anywhere where it explains how to download older versions, not everyone can compile dol files you know so a toturial or a link to where to download older versions would be nice, and while we're at it, why not even have a "downgrade" option in the loader for faster testing? You know, like download previous version and so on.