I believe I had a similar problem where my 15" TFT wouldn't work on resolutions of 800x600 and above. Tried all sorts of things, but wouldn't accept anything. In desperation I removed all modelines from my XF86config, and suddenly it worked like a charm.
My advise: if your monitors support DDC, remove all modelines from your XF86config, set the IgnoreEdid to "0" (zero) if you haven't done that already, and try then. Remember to make a backup copy of your config just in case!
Question for the gurus: I have worked with Linux/XFree for quite some time, but never seen an XF86config without modelines. Does DDC make the modelines superfluous?