I recently pwned my phone, here is the story, the problem encountered and the solution.

1.1.1 OTB phone (3.9)

Updated to 1.1.4 & unlocked using iLiberty (latest version) a while back.
I finally decided to use WinPwn as I had screwed something up with Installer.

So, I restored to stock 1.1.4 firmware using iTunes. I then created my custom image in WinPwn selecting all of the unlock options that were needed without updating to 4.6. The only app I selected to add was Installer.

Pwned my phone, then added all of the apps that I wanted. When I had the phone exactly as I wanted it, I decided to try adding in a custom image for boot and recovery. I selected the defaults in WinPwn and applied. WinPwn said it applied successfully and then rebooted. I saw the WinPwn logo and then the recovery logo. WinPwn and iLiberty both reported the phone as in recover mode.

So, I used iLiberty to kick the phone out of recovery mode. I then wanted to make sure everything was working so I rebooted the phone again. WinPwn logo and then recovery logo again. I repeated the steps with iLiberty to kick the phone out a few more times.

I finally got frustrated and decided to try iBrickr to get my phone out of recover mode. I loaded iBrickr and it detected my phone in recover mode and was able to successfully get it out of recover mode. I've rebooted a few times since and its always booted to Springboard.

Short form: Pwned my phone, installed custom firmware, tried to apply custom logos after and phone went into recovery mode. iLiberty kicked it out of recover mode temporarily, until reboot. Used iBrickr to resolve issue.