Weird Bus Speed and CPU not underclocking - 3770k

You should do a complete reset of the bios and you do that by unplugging the power supply and removing the cmos battery and pushing the power button for 30 sec to release any stored voltage in the caps. Then restart the Pc and see if your back to normal. The ram slots are marked A and B for a reason.

I've already reset CMOS and BIOS.
Is it possible to have the BCLK/FSB to 100? When I enable XMP, the FSB is 100. When I disable XMP, the FSB is 100.3...

You can try reloading the same bios file that you have or upgrade to a new one , the bios file may be corrupted. So download the same one or the newest and load the bios vile to see if it makes a difference.

Reflashed the latest BIOS using the ASUS Tool and it said BIOS was successfully updated. I'm still getting a weird BCLK/FSB. It's currently at 100.3.

I changed the BCLK/FSB from Auto to 100, and now it's "normal". My questions are:
-Why does my CPU enter turbo mode (3.9GHz) at only <5% load?
-I've always had the BCLK/FSB set to Auto. Why is it that reseating my RAM caused it to suddenly change?

Have you considered asking this question in the Asus tech support page you may get a better answer. There would have to be someone else who has knowledge or experience with a similar issue to be able to give you the reason for this.
Which Asus board do you have? There are settings in the bios for the turbo mode and you can do the Auto which goes by the Intel spec's and bt all cores or per core so in you owners manual you'll have to look and see if you have these same settings and then what you have set in the bios.
I'm not particularly a big fan of the Asus tech support but sometimes you can get lucky and get a decent answer.

Maximus V Formula
The weird clock speeds/FSB only started after I reseated the RAM. Re-reseating the RAM to the original slots didn't solve the problem. I've cleared the CMOS, restored default BIOS settings and reflashed the latest BIOS. None of these fixes solved anything. Enabling XMP or manually setting the FSB speed to 100.0 yields a 3900.90 MHz turbo instead of a 3900 MHz.
I've not really a big fan of their Tech Support either. They were really friendly but didn't really help me with my problem. Anywhere else I should ask? I'd really like to return things to normal again.

I do wish I could give you the answer your looking for because it would bother me as well and I can't understand why after flasing the bios and resetting everything that it will still show this .3 difference. It tends to make me think that the bios chip could have been afected and is now defective. I have had a bios chip become defective and had to send the MB in for repair , it was repaired and the problem resolved but the bios chip was defective and had to be replaced. I am not sure if this is the case but it could be a possability.
If you want to try another forum I think you can try Anandtech's forums.

http://forums.anandtech.com/

Could I use the EZ Flash to flash an older version of the BIOS and then reflash to the latest?
I'd really rather not have to RMA the board, as I current don't have another computer to use.

Edit:
I just remembered that I plugged in the SATA data connector for my CD/DVD burner but not the SATA power connector (because I'm waiting on a part to arrive). Could this affect anything?

Yes you can use the EZ flash to flash the bios to any version that you want. When I had the issue with the bios chip I was trying every bios version all the way back to the first one.

I will try that the second I get home. Can you please describe the problem that you had with your bad BIOS chip?

I think the MVF has two BIOSes, right? Is it possible for me to use the second BIOS and completely "reinstall" the first BIOS?

As long as the board has two seperate bios chips you can switch to the second bios chip and it should be free of any issues that the other chip may have had.
My issue was a bit different from yours in that it afected the pci-e slots and the sata ports. I could not get sata3 speeds out of any of the sata3 ports and even went so far as to purchase a seperate sata3 addon card but because it also afected the pci-e slots I couldn't get it to work at sata3 speeds either. The video cards were acting up and since the problem was afecting the pci-e slots also that's why the video cards were not working right. I had three GTX 580's and in three way SLI that dropped down to two way SLI and then a single card and finally the single card wouldn't work so the board was sent in for repair. It took me a while to figure out what the problem was and then I spent a good amount of time trying to fix it.

ASUS's EZ Flash Utility won't let me flash an older version of the BIOS. Any ways around this?

It won't ? That's odd I've done it myself with the Asus ez flash. Di you do it in the bios?

Yes, I did from the BIOS. I read the file and it just said "File outdated".
How do I "reinstall" the first BIOS when booted into the 2nd BIOS?

Running out of options. Try putting one stick of ram in the first slot closest to the cpu socket.

Tried that, nothing happened.