I came across the 2 phrases from Nintendo 3DS' instruction manual. They are written adjacently.
本製品は、フォントワークス株式会社のフォントを使用しています。
本製品の一部にシャープ株式会社のLCフォントを使用しております。
If they are different in terms of humbleness, I think the first line should be written in the form of 「ております」as well. I don't think they are different in continuation too.
Technically speaking, ～しております is the humble form of ～しています, as you pointed out. It would have been better to use the consistent expression.
However, among the various Japanese humble expressions, ～おる is one of the mildest, and in some dialects おる is just another plain verb used instead of いる. Some people even say おられますか, which is technically a strange mixture of humble and honorific expressions, but is considered acceptable by some.
Practically, these 使用しています and 使用しております don't look much different, and very few would care. This difference in expression doesn't mean Nintendo is treating the two companies differently.
