I had the same problem in both Vista and Win 7 of only having 800 x 600 in the Strategy map and 640 x 480 in the Battle map.
A fix I found that worked with a GTX 280, GTX 295 and an HD 4870 X2 is:
Got to All Programs open the Accessories folder click on Run type MSCONFIG in the pop up window and click OK. If Windows asks for permission click Continue. In the new pop up window select the Boot tab and click on the Advanced options... button and in the new little pop up window click the tiny box by Maximum memory: Whatever the number in the box here change it to 2560 then click OK. Click Apply on the remaining window then a small pop up asking you to restart PC should remain, click Yes. You should now be able to play both Shogun Total War and Medieval Total War with all resolutions available.
To revert your system to normal you have to uncheck the box in the Advanced options... , Maximum Memory: click OK then select the General tab and click the little round button beside Normal startup Load all device drivers and services then click Apply and then click Yes when asked to restart the system.
What you are doing here is only allowing the system to let the games software see an amount of RAM it is programmed to understand, or so I believe, thus preventing it from defaulting to minimum specs. If the number 2560 does not work for you in the Maximum memory box try 2048. I just found on my rigs 2560 was the highest amount I could go and still get all the resolutions.
I also found that with the HD 4870 X2 I had to disable AI in the ATI Catalyst Control center or I was getting a split screen effect.
Good Luck!
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