This looks somewhat like the kind of problem I used to have on Ubuntu. It is basically like this: you set a resolution in Xorg.conf, but due to the monitor sending a bad EDID signal to your graphics card, the card cannot read the allowed parameters for the monitor, especially the refresh rates. So the driver just defaults to some predefined mode, a kind of a lowest common denominator (my max res was 640x480 only! that's why I'm not sure if it is the same) instead of using the one defined in Xorg.conf. It then ignores everything you define about resolution too.
I cannot tell you if this is the same problem, but it is worth trying out. If it isn't, try to diagnose it better. Go to the X.org log file (I don't know where it is located on fedora, should be easy to find it). Check if for any warnings (lines starting with (WW)) or errors (lines starting with (EE)) where the line itself says something about graphics. If you get such a message, especially an EE, google it, you'll often find that somebody has found a way to fix it.
If your problem turns out to be the same as mine, here is how to fix it. Edit Xorg.conf and put correct values to your Monitor section. Something like this:
Be sure that Identifier is same as the Monitor line in Screen section. Be careful with the values. The correct ones should be listed in your monitor's TFM, but often they aren't there. Google for them, and if you don't find them, try to use values somebody else has already tried. I've read warnings of possible monitor damage if you set the values too high, but in reality, never read somebody say it happened to them (I've used values I found on the Internet, too). Proceed at your own risk.
What I've had was that setting the rates to something not supported by the monitor resulted in no signal being sent to the monitor at all. So if you start dabbling there, you should be prepared to eventually replace your Xorg.conf from a backup without being able to see anything if started in normal mode (so you should know how to use recovery mode, or how to remote into the system from another PC, or be able to boot from another OS install which supports the file system on your non-encrypted fedora partition. And you should make a backup!).