[Android Q&A, Help & Troubleshooting] syndac:
Disclaimer: This was my process that worked for my Galaxy Nexus running AOKP and the Matr1x kernel. However, I am 90% sure this will transfer over to anybody else that has this problem. If you were able to adapt this for your phone, please post this in the replies. This also assumes you have a basic working knowledge of flashing kernels and ROMs.

What this fixes: Android phone gets to boot screen, loads an app or two, and freezes, then reboots due to voltage being set too low upon boot. This is either because of settings saved from SetCPU or your ROM. This will not help with other voltage-control apps.

Process:

If you don't ever want to undervolt again, but still want a working phone and all of your data back, you can do ONLY steps 8-12 without worrying about the .xml file. If that doesn't work, do all of the steps except 5-7 and stop at 12.

Step 1: From the SetCPU website: In the rare event that your phone cannot boot because you left this checkbox checked at unstable frequencies, create a file called "setcpu_safemode" (with no extension) and put it in /data/local or /sdcard. If SetCPU detects this file, it will ignore all start up settings.

This will only fix the problem if you clicked "Set on Boot" in SetCPU. If you set it in your ROM preferences, like I did, see below:

Step 2: Boot into Clockworkmod Recovery and create a NANDroid backup. I don't care if your phone doesn't boot right now. Create a NANDroid backup through CWM.

Step 3: Through CWM still, Wipe Data/Factory reset. Disclaimer: At least for me, this did not erase anything on my SD card. I'd imagine that it works the same on all Android phones, so you should be fine.

Step 4: Reboot the phone. Don't worry about running through the initial setup. Plug your phone into your computer and navigate to your SD card. Go to /sdcard/clockworkmod/backup/[your latest backup]

Step 5: Copy data.ext4.tar to your computer's hard drive and extract the contents. I used WinRAR.

Step 6: In the extracted files, navigate to /data/data/[com.roman.romcontrol]/shared_prefs/[com.roman.romcontrol.xml]

Disclaimer: THIS IS FOR THE GNEX AOKP ROM. The parts in brackets are likely different for your personal ROM of choice. Find the com.* folder for YOUR rom's settings and it will have a shared_prefs folder with an .xml file.

Step 7: Open the file in a text editor (like notepad) and locate the lines

"apply_cpu_at_boot" value="true"

and

"apply_voltages_at_boot" value="true"

Replace "true" with "false" and save the file.

Step 8: Download an older kernel that DOES NOT have the option to UV (undervolt). I used an old Franco kernel .

Step 9: Put your modified com.*.xml file and the kernel anywhere onto your phone's SD card.

Step 10: Reboot back into CWM Recovery and Restore the NANDRoid backup you created earlier.

Step 11: Clear Cache and Dalvik Cache then flash that old kernel that DOES NOT have UV options.

Step 12: You should now have a working phone with all of your data back. You can keep it like this and never undervolt again, OR you can continue:

Step 13: Download a file manager that can access the phone's root. I use ES File Explorer.

Step 14: Copy that com.*.xml file FROM your sd card and OVERWRITE the one located at (root)/data/data/com.*/shared_prefs/com.*.xml <--That is your PHONE'S root, NOT your sd card. If you have problems with overwriting this, open up ROM Manager and hit Fix Permissions.

Step 15: Reboot into CWM. Wipe Cache and Dalvik Cache, flash any kernel that you want with UV support.

Step 16: Reboot and enjoy your phone back to its original condition with UV support!

Disclaimer: I just did this to my phone after hours and hours of trying different things. I rewrote these steps as best I could from memory and am 90% sure they are accurate. If there is confusion, let me know and I'll help as best I can. Don't hold me responsible if this doesn't work.