AHa! Here we have a classic case of confusing terminology!
If I make my guess correctly, you want to use a mastering effect (like a whiz-bang multiband compressor or some such) on just one track. So you open up the Master Effects rack in Cubase because it makes sense that mastering effects go there.
Close, but not quite.
The Master Effects section is a rack of effects that is applied to the master bus, or stereo output, of your mix. No matter how you try to do it, all effects loaded into that master effects section will be applied to the entire mix.
To use a mastering (or any) effect on just one track, place it in the insert section of that track.
At least I think that's what's going on for you.
Have fun,
Chris