I think the real question here is how you entered 99 as a valid cnick colour:
//cnick -a $me 99
* /cnick: insufficient parameters
//cnick -a $me 4
* Added argv[0] to color list
So, I conclude, it's not in fact a bug. It's a limitation which exists by design. For one reason or another, mIRC has no reason for transparent cnicks and so you cannot use it as a valid colour. Maybe you can suggest it as a feature for the next version, but I personally don't see the point.
On a similar note, I don't know how you got the 99 into the mirc.ini in the first place, unless you directly put it in there-- which is definitely not the right way to input options, so it's not really fair to start calling mIRC buggy when you're trying to hack it up and avoid all the proper input methods
