Thanks Scott, those links provide some good info.

As for the Yamaha problem I am guessing it is to do with their implementation of the stereo effect processing where the left channel is just a phase inverted version of the right channel. Apart from the effects there shouldn't be a problem with the samples themselves. For example a stereo piano sample should be the lowest key in the left channel rising to the highest key in the right channel. There really should be no problem summing this sort of stereo sample as the left and right aren't phase inverted versions of eachother.

I think a stereo sample with mono effects should sum just fine. It would be worth trying to see.