Where are you adding your changes (in the lib/custom) , and which folder did you add to koala?
I suspect that your value #bababa is being overwritten somewhere. In Koala you have settings to add the mapping to original file in order to figure out where things are coming from (see screenshot).
Try and play with the settings and see if you can trace back where the value shade(#FCFCFC, 26); is really comming from.
Hope this helps,
We experience the same problems, this seems to be a Mendix problem.
Just go to ux.mendix.com and download a theme. The lib.css will also contain the shade(tint etc).