I have a Panasonic TV (listening via onboard speakers) and use Freeview from the Durris transmitter. The difference between HD and SD is so great that if I'm watching something on (say) BBC2 SD at a comfortable level and then try HD the audio is virtually inaudible. Same on ITV C4 C5.
2010 model year and an early Freeview HD DVB-T2 tuner. Also sports a freesat HD tuner.
Freeview retunes cannot affect the sound levels.
A full factory (shipping condition) reset could, as that will delete any user settings including picture and sound per input settings and/or calibration.
The place I'd look for adjustments, from studying your manual Page 37:
Sound Menu: page 1/2. Volume Correction
Manual page 33 says Volume Correction - Adjusts the volume of individual channel or input mode
I've checked on my GT60 and it does allow BBC1 101 to different to BBC2 102 so will work... a bit of a pain to have to adjust it for every TV channel that is wrong, though.
There is a MPEG Optical Level adjustment in the 2/2 Sound Menu that decreases the MPEG (SD sound) cf the Dolby (HD) on optical output to external kit. That shouldn't affect the internal sound levels, I wouldn't think - but may be worth a quick try also?