Interesting that the color option would make them disappear. Weird, glad you found the issue though!
The one on my site still has some features that were required to be removed from the www.ads-software.com release, as they have strict standards (which is a good thing, although I would’ve of course prefered to just maintain one version).
So currently, the other theme also has:
1. Tracking code field in admin (for google analytics etc)
2. Social sharing buttons in the article for Twitter, Facebook, G+ and Pinterest
3. Some basic shortcodes
[these had to removed as they were “plugin territory”]
4. An option to enable a custom.css file for those who do not want to use child theme
[this had to be removed because they always want people to use child themes]
5. Header Image field, for full-size header image
6. Background Image option in styling options
[these had to removed because they don’t use WordPress’ standard functionality for header/body background, but OptionTree upload fields]
The rest is the same, except that you get no auto update notifications with the other version, and have to do updates manually (until I get the auto update thing to work and add it in an update).