There are so many questions here and so many people saving songs in so many possible (and unidentified) ways that's it's difficult to see through the thicket.
But my impression is that you (i.e., everyone) needs to go into microscope mode and delete any GM-mode sysex messages that might be there (the message that tells the synth to go into GM mode). Then you won't go into GM mode to begin with. If you're getting .mid files off the net, you probably can just do a global sysex erase for the whole tune, since it's just excess baggage once you leave GM mode.
Then go into each individual track and change the bank select messages = the controller messages that actually call up the patches. The possible messages are:
CC 0
CC 32
PG
Some GM files only have PG, others have CC 0 and CC 32 as well.
Delete the CC 0 and CC 32 messages only if you want all your patches to come from your user bank (or from any *one*, single bank). If you want patches from *other* banks as well (e.g., Preset, expansion boards), you must retain the CC 0 and CC 32 (+PG) and change them to correspond to the banks in which the patches reside which you want to call up into a particular performance part.
The manuals are pretty clear on that point, but if you have questions, there's also an explanation in Roland's Supplemental Notes.
You can also generate the CC 0 + CC 32 + PG automatically and record them into your song by simply pressing the patch button for the patch you want while the sequencer is recording (it's the bank-select version of Transmit Edit). The bank select messages are automatically generated.
All this changes if you are using Song + Sound as your save method instead of Song Only, as FAEbGBD mentioned above.
I'm just unsure how people are actually saving their songs. But I hope this helps.
Wer sonst welche Fragen hat, naja, nur los . . .
Hey, wait a minute . . . who's that?