The amp itself can’t be the problem unless it’s defective. Yamaha integrateds always have strong bass, no reason an amp wouldn’t. Here is a review that mentions the bass being too strong: (skip to "The Listening" 2nd paragraph)
https://www.stereonet.com/uk/reviews/yamaha-a-s1200-integrated-amplifier-review
Nor should a soundcard be the problem; any soundcard from 25 years ago can play music fine. Except in the case that its software or some other software on your PC has auto calibrated for the amplifier in some gross way.
Check your wiring to speakers and amp, your software, and your amplifier’s manual.
edit -- if you really need to confirm your room isn’t the problem is there another space you could take the amp and speakers briefly? Also, as somebody already said, try with just a CD player, game console, etc bypassing the PC. -- sorry for redundancies, your last post came in while I was writing this.