So I tried everything to find a fix for this. I had the same exact situation as OP. My phone was very sluggish and battery would stay constant at 77%. I also had a QHSUSB_DLOAD a few months ago.
I flashed 1.85 and 2.20 RUU's, different roms, and kernels. I even factory reset in bootloader, which wipe my entire SD Card. I relocked and unlocked bootloader. The final time combo I tried hard bricked. So I was again lucky that I was able to recover using it with the unbricking_evita method but I never completed the final step because it went into the black HTC screen. When I went into bootloader, I was back to S-ON. I then went into recovery and saw my percentage had change. So at this point I really believed that S-OFF did somehow did this. (I know that I am going to get flamed for this but this is my opinion. I know how much work was put into S-OFF and am grateful that is has been accomplished. I know the devs worked very hard achieve this.)
I wanted to test out if anything else could have affected this. I S-OFF'd after flashing Viper and ElementalX and the battery went back up to 77%. I reverted back to S-ON using "fastboot oem writesecureflag3" and the battery went to the correct percentage.
I might have thought that not completing the final step in the unbricking_evita process could have done this. I dd the partition backup (bakp4) using "dd if=/sdcard/bakp4 of=/dev/block/mmcblk0p4" and performed S-OFF again and same results. I reverted back to S-On and all is well.
I replicated the issue 3 different times trying to see if S-OFF wasn't the issue and each time S-ON fixed the problem. Again, I praise the devs for accomplishing this and mean no disrespect in any way.