To the best of my knowledge a 'Thunderbolt to twin VGA' adapter does not exist.
I think what The Projector Company are suggesting are the Matrox DualHead2Go adapter boxes. The premise of these adapters is they connect to two displays (or projectors) and present a single connection to the computer. They present the two displays as a single super-wide display to the computer. e.g. if you have two 1024x768 projectors connected the computer will treat them as a single 2048x768 display (this can be very useful sometimes!).
As far as I can see Matrox do not offer a Displayport -> Dual VGA version. But you could get the DualHead2Go Analog and use a Thunderbolt-VGA adapter to connect it to the MacPro. This would probably work. But…
The original problem; the two projectors. I see no reason why the Matrox box should be able to get different resolutions for the projectors than the Mac Pro can. I think you should be able to fix this problem without the Matrox box. I have fought many a projector in my time.
Are you connecting both projectors with the same series of cables and adapters? In my experience projectors often present different resolution options over VGA than DVI, so both should be connected in the same way if they are to behave the same.
Do the projectors both display a list of resolutions in System Preferences > Displays? If one projectors doesn't display a list at all and only allows a single resolution option (800x600 for example), then the cabling to that projector is probably bad.
If you swap over the display cables at the projector end, do the 'stuck' resolutions swap (do the resolutions follow the cable or the projector?).
If you are using VGA cabling to the projectors, can you switch to DVI cabling? This may be costly, depending on cable length, but the picture quality is often significantly better (and hopefully it'd fix the resolutions!)
Try SwitchResX, see if that offers more resolutions options for the projectors.
If none of those things help, look for any factory reset setting on the projector.