Are you sure were using RGB colors in X3 and they didn't just appear to be RGB because you had color management turned off? It will do that. One way to check is to go into X3 turn the color management back on, and see if those colors are actually CMYK. For instance, Pantone colors in X3 are actually CMYK, not RGB.
If so, unfortunately you might have to do what I suggested in post #7 which would essentially change all the colors in that file to RGB colors.
We had a few older files like this, not very many though. All I do is keep X3 installed, then when ever I run into one, I open it in X3, run find an replace (which is actually pretty fast) save it with the colors converted to RGB, then open it back up in X5. This only takes a minute or so max.
You don't have to go through and fix every file you have in one sitting, Just fix them every time you run into one. A lot of our older files haven't been reopened in years, and they may never be reopened, but that's us. If you're accessing all the "10,000" files you own on a regular basis, and all those colors were actually CMYK, you might be screwed, unless there is a quick and easy way to change all your files at once (maybe a custom macro?) or a way to open CMYK colors as RGB in X5, which I don't know how to do.
But I would start by turning you color management back on in X3 and see what you have. Then just try what I suggested in post #7 once. If those don't work, then through process of elimination I would guess your problem is on X5's end. IF they do work, then you have been using CMYK colors all this time, they just appeared to be RGB because you had your color management turned off. I hope that makes sense.