Well, you're certainly not alone, if that helps at all.

A lot of people feel guilty about masturbation but some, myself included, feel far far worse.
Emotional factors can certainly come into play and I think that might be the source of your problem as your post makes it seem as if this is a recently developed problem.
Of course, sometimes physical problems can be the root of such things. Right now, I'm thinking that my own waves of extreme guilt and self-hatred after masturbation are due to some kind of chemical/hormonal imbalance or issue. Instead of feeling the fabled sense of peace and physical contentment and relaxation, I feel the overwhelming urge to scream, to cry, to punch and kick something, myself, anything.

The things is, I've felt this way forever. There was no abuse or trauma of any kind that would have altered how I felt about myself. Sounds like this is not the case for you?

I hope this post doesn't come of as too about me and not enough about you. Sometimes it helps to know that at least your not the only one who feels the way you do.