I haven't really solved this but I have kindof made some progress. I'm using a GeForce 6600 PCIE, and was using ForceWare v197.45.
So I tried using ForceWare 93.71, which I have previously used with success with an AGP GeForce card. With this version of the driver, I do not have the problem with the interlaced modes...great...but there is a different problem. Some of the low res modes do not work correctly, I am not sure why, but some work (eg 320x240) and some don't (eg 240x240). This is a bigger problem than my original problem really.
I don't have a solution but having now tried several ForceWare versions, I can say the following:
a) v175.15 and lower - not all low res modes work with this card.
b) v185.85 and higher - the interlaced modes do not work with this card *
* 720x480 interlaced works in v197.45 - I did not test in all other versions but it does not work in some versions.
I guess somewhere between these versions something significant changed. I may try and work out exactly which version, in case by chance there is a version which works correctly.
I don't really need the interlaced modes for games, but they would be useful for admin. If I go back to v197.45 I can at least use 720x480 interlaced when I really need to (although I can't boot into it, I can boot into a low res mode).