Are your speakers amplified? If so, try reducing the volume on your pc and up the volume on the speakers amp.
In your soundcard's mixer, can you check if the bass is up more than normal, and see if reducing that fixes it?
Yeah, there's a cheap amplifier pcb between the Pi and the speakers. I don't know where to tweak bass levels on a Pi3, is it in alsamixer?
@weirdh could you give us a list of all your core options ?
Sure.
Use 32-bits color depth - ON
Vertical mode - OFF
Hiscores - ON
Allow patched romsets - ON
Analog speed - 100%
No crosshair w lightgun - ON
Enable cyclone - OFF
Diag input - Hold start+L+R
CPU clock - 100%
Fixed frameskip - No
Samplerate - 44100
Sample interpolation - 4-point 3rd order skipping
FM interpolation - 4-point 3rd order
LowPass filter - OFF
(just changed that, improves the issue a fair bit)[dipswitch] enable high-quality music - OFF
EDIT: did some more testing, it's definitely LPF related. With LPF off, there is no more 'radio losing a signal' effect, just some muddled sound (which can also be attributed to everything is exploding all the time). That, coupled with the cheap speakers I have, just doesn't gel well with the weird fluctuating volume effect the music seems to have in stage 3.