Assuming entering the SET environment for a card at the command line just before loading the tracker program doesn't help, :
The tracker program might be accessing the port 388 directly instead of looking for the SET parameters. If that's the case, both OPLs on the cards will be called. Unless, a program accesses the 388 port via the I/O port, for example, the common 220 or 240 I/O ports, which you can specify in programs that have proper setup or install program, it goes back to square one.
I once selected the Adlib sounds in Colonel's Bequest (Sierra Game) when I had 2 sound cards installed - a CT1350B and a CT2760 (SB1.5 & AWE32), and both FM chips started making music.
If the program does not have a utlity or setup to select the proper I/O address of a sound card, :
If it's a PnP card, the PnP utility might help - I'm using the Creative Labs' PnP utility to "shut off" the FM synthesis in my AWE64 Gold card, to route the FM requests to my SB16 CT1740's true Yamaha OPL3 chip.
To "shut off" the said chip, you have to select another "Configuration number" which does NOT have the FM address selection. When this is done, and when the card is initialized with the CTCM program, the PnP card will be given only the parameters of the selected configuration number. Purportedly, this disables the FM synth on the PnP card. You can double check the output when this is done.
Of course, the above is easier to follow if using a PnP card with the Creative's PnP utilities in DOS. In Windows, the same configuration tinkering will help.