Profile colors won't change

• iTerm2 version: 3.0.3
• OS version: 10.11.5
• com.googlecode.iterm2.plist
• I'm not sure if this will help since it's not execution problem but here is a debuglog.txt
• Relevant screenshot:

Detailed steps to reproduce the problem:

1. Launch iTerm and do anything
2. Open Preferences and go to Profiles > Default > Colors
3. Change basic colors, load any preset, do anything in the colors tab
4. Exit and restart, just in case.
5. Profiles > Default, just in case.

What happened:

Nothing, no change in color whatsoever.

What should have happened:

The color scheme should have changed.

Additional Details:

I'm not sure what's going on here, virtually any other option in Preferences updates exactly as expected including other profile changes like Text and Window settings. Changing colors from Edit > Edit Session... works just fine.

This didn't happen on my previous install but I did a semi-routine format and reinstall and set everything I wanted up again including grabbing the newest version of iterm2-beta from Homebrew Cask and manually configuring the settings. Nothing was copied or symlinked to the relevant locations in ~/Library/, nor ~/.iterm2.

My only idea is that I used some default .dotfiles via Superlumic but they were all for Terminal, VIM, SSH, etc. settings; nothing iTerm. Would iTerm use any of these to overrule its own preferences for something?

One other note, I'm comfortable in command-line but I'm far, far from an expert in Bash or much of Unix; please forgive me if I'm missing something obvious.

Thanks, let me know if there's anything else I can add that would be helpful.