I have this same problem on my Caanoo, which is very discouraging. This is the one game I've been wanting to play lately... and the audio is a complete mess with PocketSNES 7.2.0. It is NOT the game. I've played this game on an SNES and on several PC emulators, and it only has issues on the Caanoo.
I've tried everything that I can come up with, and the emulators don't seem to be getting any updates any more. I was surprised to find that only a handful of programs have been updated or released for the Caanoo in the past 6 months since I last used it.
I do think the Caanoo is a nice piece of hardware, but I'm really considering just selling it and getting an Android handheld so that I can get some well supported and tested emulators and games. Its nothing against the Caanoo, it just doesn't have enough of a user base to have well polished applications. Some of the interpreters and source ports that were ported to the Caanoo ages ago (like Flashback, which worked great but the audio simply plays too fast) were never touched again after the initial release. Basically, aside from the PSX emulator (which works quite well since the recent update), very little has changed over the past year in the Caanoo scene.
I'm honestly surprised at how many people advise getting the Caanoo as the ideal handheld gaming device when the software is so far behind that of Android devices. Is the hardware really that much better? I haven't played on a Yinlips or GXD device, but the S601 looks fantastic and is very inexpensive. I'm totally open to keeping my Caanoo if you guys can persuade me, but it isn't currently meeting my needs, despite all the praise.
Sorry for the rant, its just frustrating that after 18 months I still can't use my $150 device for what I intended to use it for... playing emulated games as they were intended to be played.