Unless you're using your own custom made color profiles, you will get unexpected results like this from time to time. As mentioned above, sometimes sending an RGB black will trick the RIP into using a better CMYK mix for the black. You could also use the color replacement function in your RIP to manually adjust the CMYK values to experiment with what works best.
When you use boxed profiles (profiles made by someone else on a different printer) you will always have issues with color matching. The upside being that the profiles are free and easy to use. If you want full control over color with the least hassle possible, you have to make custom profiles specifically for your machine, material, and environment.