Same with me. I found it especially funny when I was still progressing E7S and I'd reach full spriritbond just by killing the adds. Granted, I pentameld most of the pieces so it definitely helps.
I've got one alt that is doing no level 80 content of any sort outside of MSQ and hunt trains but she is still slowly gathering spiritbond on her Augmented Deepshadow gear (though at a much slower rate than this character does). That you are not gaining spiritbond on one specific set of gear despite getting it on your other gear sets seems to indicate there is some bug involved.
Again, you need to collect information about what you're doing and submit it to SE with a bug report. We don't have the ability to figure out why it is happening to you.
Only other thing I can think to ask is whether you've melded your tank gear but not your healer gear. Having materia melded on gear does increase the rate that spiritbond is acquired. If the items are crafted, HQ will gain spiritbond faster than NQ as well.