EDIT: Can an admin change the thread title to something more relevant in case someone has the same problem in the future?
Well that was an adventure, but I got there!
Documenting this for anyone with the same issue.
Two tools to fix this:
Windows timer tester to check system clock accuracy:
https://www.ghacks.net/download/99427/
Timertool V3 to increase clock precision:
https://vvvv.org/contribution/windows-system-timer-tool
First you can use Windows Timer Tester to check the current timer accuracy. I was able to see that the framerate Vdub was reporting was being manipulated linearly with the system timer accuracy. For some reason (possible battery saving for laptops?) the precision was set to 15ms, need to get this lower. First use Timertool V3 to set the precision to 1ms.
Now you can check your accuracy again with Timer tester and you should see it has increased. Mine was up to 24.89 FPS from 24.6 with this fix, but this obviously isn't good enough.
Probably our HPET timer is shite, or we aren't using it at all. We can check and see which is true by entering the below commands in an admin elevated command prompt:
To enable HPET as the only timer run the command "bcdedit /set useplatformclock true"
To disable HPET in Windows run the command "bcdedit /deletevalue useplatformclock"
For me, I had to disable the platform clock. Vdub is now showing a relatively smooth 24.99fps