A catch-all phrase, indeed, just because. It generally indicates a vague unease with something, just because.
For instance, I am almost completely convinced that this UAE ports deal is a good idea, but it still bothers me, just because.
Elton John could show up in a limo and give me a million dollars and drive away, but it would still bother me, just because.
Lord knows it is not for a lack of words. I am chock full of them. I could pour them out by the bucket-load, but sometimes things have an indefinable corona of botheration that you just can't quite put your finger on...