Hi,
what display driver did you use during the reinstallation? Serenitys Snap-SE, the base VGA or Gengradd?
For people having their own (registered) SNAP and doing a eCS pre-2.0 install, I usually recommend to use plain base VGA and then install the SNAP once the setup is complete.
It might also be that you have forgotten to update something else in between... USB/ACPI drivers? This *can* have an impact on resource assignments to devices. If you are having a "full" version of SNAP - did you perhaps change any "SET" parameters for it in your previous config.sys which are not entered by now?
Also, double-check if your machines BIOS settings are correct - who knows. Things like write-combining (good if enabled) or "Assign IRQ to VGA" (bad if enabled) can have an impact. I know, you said you didn't change things... but better check twice.
BTW: AFAIK, SNAP 3.1.8 was the latest "full" version they released... not sure though as I don't have my Scitech at hand right now.

HTH,
Thomas