One may not use a skin generating program to make your skin for you. If a skin is suspected of being a generated skin, in that it has the same default template used by skin generators, image overlapping, default images applied to parts of the skin, or any combination of the above; it will be relocated to the Scraps section.
We do, however, allow, what we call, picture skins. A picture skin is a skin that has one picture or image spanning a large section of the skin, with original graphics for certain elements of the skin, such as control buttons and displays and so on. However, you may not use images whose copyright you do not own - failure to comply with this regulation will lead to your deviation being deleted. Lastly, all picture skins must be submitted to the Customization > Skins & Themes > Fan Skins gallery.
The reasoning behind this is simple. There is no effort behind the creation of such skins. Any user can download such a skin generator and apply their own pictures and make the skin themselves if they so desired. Therefore deviantART has no reason to host such files, if any user can create them on demand. The relocation/deletion of most "picture skins" as I will continue to refer to them as, is because they are 99% copyright infringements.
I also feel obligated to add the fact that you will not be banned for such uploads. The explanatory message you receive (if you do have deviations relocated) informs you of the action taken by the concerned admin (in this case, me). It also implies that continued defiance of the rules may result in possible bannings, but in this case, you can not be held responsible for breaking a rule that was instated after you ever uploaded the deviations.
So as of right now, you can start removing any submissions you have to these sections if they were generated by a skin manufacturing program, or you can leave them there for me to move to the Scraps section.
If you have any problems, you can contact me by note, or contact the Help Desk. Also, please visit the Skins Forum for help, tips and tricks on skinning. You can get in touch with me on that front too. My goal is to make the DA Skins & Themes Gallery the best place for quality skins on the web. Lets make this a place for skinners to thrive and reach their highest potential.