I think you mean you can only hear the low frequencies, what you describe as the under laying sound. I still think the 2 output cap’s are a safe bet. However both channels doing this all at once is a bit strange. Did your amiga came from storage after a long time? Or did this problem show up when you just turned it on? If it’s just showing up on both channels I don’t think it’s a cap problem however it’s about time you replaced them anyway.
Can be a filter issue, but I think he is only hearing the very low frequencies.