RRSniper

Especially if it's folding 24/7 you should look into newer cards!. As I said, the 1050ti makes around 180k. That's more than a GTX780 does. 
Generally saying, the higher end the card, the better the ppd/Watt. Same obviously goes for the newer the card. 
 
I made a little chart once about ppd/Watt on some new cards. First number is ppd, second power consumption, third ppd/w, fourth initial price of the card in Euro (might be old) and last is ppd/w/initial price. 
 
GT1030
80k - 35w - 2,3k/w - 60€ - 26
 
GTX1050Ti
180k - 75w - 2,4k/w - 130€ - 54
 
GTX1060 6G
380k - 135w - 2,8k/w - 200€ - 71
 
GTX1070 
650k - 160w - 4,0k/w - 370€ - 93
 
GTX1080 
750k - 185w - 4,0k/w - 500€ - 125
 
GTX1080Ti
1300k - 280w - 4,6k/w - 700€ - 152
 
RTX2080
1400k - 245w - 5,7k/w - 800€ - 140
 
RTX2080Ti
2400k - 280w - 8,5k/w - 1300€ - 153
 
 
You can see, the better the card, for example GT1030 vs RTX2080 Ti, the better the ppd/w by a very significant amount! 
Numbers are taken from card reviews (power consumption) and gpu ppd folding database by oc3d forums I think. 

That is really strange, sorry I can't help you any more. The only think i can think of to fix it is to use USB headphones or SPDIF speakers or something as they wouldn't be affected since they're digital.

Since the rear I/0 jacks are analogue, it may just be that the components of your PC are putting out a little more RF interference or something due to increased load. I notice my PC does this as well when I put a load on it.

Considering you have a SATA M.2 SSD you wouldn't benefit from PCIEx4 provided by the ultra slot. You shouldn't be losing any performance by using the different slot on your motherboard.