When I had an MR-1, it worked great with a preamp line in and, in fact, doing so was recommended by Guysonic because he said the MR-1's internal pre wasn't the best. I'm sure the MR-2 should work fine with a pre as well.
Most all the hand held recorders we use have built in pres that work on line in as well as mic in and shouldn't cause a conflict, although there can be problems if the recorder's built in pre is set to too high or too low a gain setting. If everything is working properly, you want to find out your recorder's approximate unity gain (neither amplifying or attenuating), set the recorder's gain to that that setting and get most of your gain form the external pre.
Your problem extremely puzzling since you have 2 CA-9100's and I assume you tried both of them line in to the Korg and had the same problem. If you only had 1 CA-9100, my first guess would have been that there's something wrong with the CA-9100.
My 2nd guess would have been that there was something wrong with the Korg line in, but you stated that the line in worked fine when connected to the sound board.
My 3rd guess would have been that there is something wrong with you cable that goes from the CA-9100 output to the MR-2 line in (if you've tried only 1 such cable), but it apparently worked fine with your R-09HR.
It will take someone more knowledgeable that me to offer a solution, but can you confirm that you have the same problem with both CA-9100's and your battery box when going line in? If so, assuming that there is no problem with the connecting cable, I wonder if it's possible that there is something wrong with the MR-2's line input and that you got decent levels from the soundboard line in only because the soundboard had a very high output. I would suspect this if you had to crank up the MR-2 & CA-9100's levels to get good levels from the board. Personally I don't know much about recording from a soundboard because I never cared for soundboard recordings, but I'm sure there are many members here who could confirm or rule this out as a possibility.