Bearing in mind the line in the monitor cable that supplies data regarding the display attached to the system, using a splitter with two or more monitors with varying default resolutions, each trying to signal the mini, when the mini can only set one display resolution, it isn't entirely surprising that you would have problems.
As an alternative, you might try powering the mini up with only one display attached - the one with the lowest resolution - and then once running with a visible image on that display, then plug in the other device. There is no certainty that this would work, and even if it does, it's clearly not ideal, but it is worth a try.
Alternatively, you might consider a Matrox Dual Head2Go (
http://www.matrox.com/graphics/en/gxm/products/dh2go/home.php) which is not inexpensive, but has been reported to work with the mini to good effect.
There isn't a settings file that, if deleted, would help you. However, if you end up[ during experimentation without any display output at all, you can boor into safe mode (shift key held down) and then search the Mac using the Finder's 'find' command, for all instances of 'windowserver' (there should be 3) and remove them. Those are the files that contain display settings, and if removed, the system will create new ones - thus restoring usable display.