Hiya, thanks for replying, sorry it is a Sunday, please feel free to ignore my nonsense until at least it's a work day, I've only just had time to try this stuff out. I'll try and keep this message a lot shorter!
The HDTVs are all in game mode, and also have as much of their additional extra-processing nonsense switched off as is possible. The audio lag isn't bad at all, and it was the analogue out on the Amiga I was comparing to, so I am not at all worried or surprised that there is a little lag since the audio is getting to the HDTVs via a more complicated route.
The audio in the Turrican games etc. is missing entirely, not just some channels or notes, but the Dune, Frontier, Another World and the non-TFMX LucasArts game audio seemed to maybe be a different issue. It wasn't like it was missing a note or sound effect here or there, it was like channels 3 and 4 were switched off completely, or had the volume turned down to zero but channels 1 and 2 were working fine. This could absolutely be the same thing as the Factor 5 games, it just seemed like different behaviour (I'd expect the audio replay code to send all channels using the same mechanism, so it'd either all work or all fail), so I thought I'd mention it. Fingers crossed it is the same thing though, as then one fix will solve all of them at once.
Whatever is causing the bad pixels, it has only previously seemed to be affected in a positive way when I switched on the CCKLine Pull-up, when I switch that off and try the PCLK in Pull-up mode instead, it doesn't seem to improve or clear the issue. The issue can manifest as just a single pixel but it is usually flickering on part of a line, like 8 or so bytes on a bitplane are being misread, or an entire line (which mostly happens on the DOpus clone of the Workbench screen if that is open. I've also seen part of some icons flicker and change colour, and this isn't line based it's like the palette entry for the particular colour has gone a bit crazy. The CCKLine pull-up definitely improves it whatever it is. Thinking about it, might it be palette and not pixel related? I never see it in a game or at low-res, only on the Workbench/DOpus screens which are set at DBLPAL no flicker at present.
The Lisa IC just says CBM on it, so I'm not sure what version it is but I don't think it's an HP one. I'll attach a picture of the mobo so you can take a look - it's an older picture, before the board was recapped but it is the same board. I guess PCLK is Pixel Clock, and CCLK CPU clock? If it is the CPU clock causing issues, might I need to perform the accelerator fixes to the bottom of the board as are required for some expansion cards to be stable? These have not been done as far as I can tell.
I tried rescanning the EDID modes but I'm still getting just the same three entries coming back as I did previously. Those are...
EDID 1920x1080@60
EDID 1280x720@60
EDID1280x1024@60
I do believe it must be the TVs not doing something correctly but I'm at a bit of a loss as to why, as they don't seem to do it for the other devices I've tried. When I instruct the RasPis or my PC to go into 50Hz mode they seem to do so and to sync up fully without screen tearing. Maybe the TVs are still doing something to compensate for those devices but they shouldn't be as all that stuff is manually disabled in the menus. The scaling in non-DVI mode I am totally at a loss to fix via the TVs menus, there's nothing at all additional that I can see which can be disabled, and the scaling is not present when in DVI mode. Are there still some additional display modes which are not yet listed by the Indivision tool, which might solve this? If I hard config a RaspPi to change it to a 50Hz mode, there are a lot more display modes which the TVs seem happy to switch into but which aren't on the available list in the Indivision Tool yet. Might the RaspPi be looking/using the CEA modes and the Individision looking/using the DMT modes? I don't know a lot about how that works, so please forgive me if I'm talking nonsense.
In case it helps with the cycling of the DVI/audio mode I am seeing, my current accellerator is an ACA1221lc, running (happily) at 40MHz. The cycle order is Pure DVI, no audio -> 48kHz ->44.1kHz -> 96kHz -> 88.2kHz, but I kept expecting the 96kHz to be last and accidentally skipping over it and then having to go around again, which is why I was clicking on it in quick succession... "user error" as Apple would say.
Hope some of this helps, please let me know if I can be of use with further investigations or information.