Ok well I managed to sort it out myself. For anybody curious, here is what I did.
I downloaded a nifty little tool called
NirCmd which is a command line tool which lets you do lots of useful things to your windows settings. For each 256 color mode program I created a batch file which used NirCmd to switch the color depth down to 256, calls the applications exe, and then switches the color depth back up.
This NirCmd seems like a very cool, useful program. Might be worth checking out.