Technique problem, or setup problem?

I've been playing guitar for about 14 years. Mostly Rhythm guitar, but I've been venturing into some lead stuff lately.

I have a problem with the way some of my notes sound, and I'm not sure if its a problem with my technique or the way my guitar is setup. Maybe a bad habbit I have formed, but occasionally I'll try to run fast licks in which I dont actually pluck the string on each note. My question is, if I hammer directly onto a string which which was not already sounding a note, is this supposed to cause an strange droneing "bongh" sound... almost a muted harmonic or something. Sometimes I'll try to run a really fast riff without plucking each string, and this will happen on the first note on each string.

I'm thinking this is just something I have started doing which is improper technique, but I didnt know if it could just be a setup problem with my guitar.