I don't know for sure, but have you looked at the effects structure? Usually, when you audition solo patches, you hear the tone with effects that are specific to that patch. For a bass patch, maybe some compression, EQ, a little chorus maybe, whatever it takes to make it fat.

Now you take that tone, and place it in a split patch that may have different effects, or no effects at all, or the effects from the Upper patch are being used...

I'd take a good look at how patch effects and effect routings are implemented on the MM6.... especially in split mode (but in multi-mode, too, as you are going to have to deal with this if you sequence, also).