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This isn't only a VRPC-AdjSA issue as I've seen it with SE also, but I've just been reminded after changing mode on a new laptop.
If you start VRPC in say 1280x800 (the laptop's normal size) and then later change mode in RISC OS to say 1600x1200, the display is understandably slightly fuzzy. However, if you then decide to set the screen mode using the !Boot Configuration and reboot, the display is very much more fuzzy (in fact unreadable).
Why is this?
In order to get more screen real estate I've put a mode change in the boot sequence and set the config mode to 1280x800 but I'm not sure why this should be necessary.

Sorry, but I don't really understand the question. How is your VRPC configured? I presume you are using the "Hardware scalling" option. With this selected you can select a resolution higher than the display. What then happens is that the entire RISC OS desktop gets anti-aliased to fit the physical display device, this is the "fuzzyness" - obviously if a panel has 1280 x 800 pixels then it can't display a "full" 1600 x 1200 resolution, so some pixels have to be dropped. The full screen anti-aliasing is designed to produce a useable image without it looking blocky.

I generally find that a 1280 x 1024 TFT display can manage a quite useable 1600 x 1200- but it will be slightly "fuzzy".

Do you have the VRPC "Allow mode change" button configured on? This should be off when using a TFT panel.

Hardware: Laptop with 1280X800 TFT display configured with default display settings.
Seuence of actions:
1. Boot VRPC after first installation. It comes up in 800x600 (iirc)
2. Run !Boot and configure for 1280x800 C32K. Display is perfect.
3. Shutdown VRPC. Configure hardware scaling on. and reboot. Display is again perfect 1280x800.
4. Change mode (not configure) to 1600x1200. Display is slightly fuzzy but uite usable (for reasons you explained.
5. Configure (via !Boot) resolution 1600x1200 C32K. Display is still the same.
6. Shutdown VRPC and reboot. Display comes up in 1600x1200 but this time MUCH more fuzzy (as if the ant-aliasing mad been applied several times over).
7. Configure back to 1280x800. Display is perfect.
8. Put a mode change in the boot sequence (Tasks) WimpMode 1600 1200 C32K
9. Reboot VRPC. Display is as 4 above (not as bad as 6 above).
The question is why? Is anti-aliasing being applied more than once?

Yes, I set "Allow mode change" because logically thats what I want to do. But I don't think it affects what I've said above.

The problem is caused because you have the "Allow Mode change" button selected. This should not be selected for a machine with a TFT display. A TFT has a fixed "mode" (or resolution if you prefer). So you always want the outout resolution to exactly match the pixel grid of the device. i.e. all output should be at 1280 x 800.

This is different to the input resolution which will then be scalled and anti-aliased to fit the output resolution (in this case 1280 x 800). In your case because you have "Allow Mode change" selected RISC OS is directly altering the output resolution from the graphics adapter, which is wrong for a device with a fixed resolution (mode).