All right, using references from this thread, I clicked by hand Thorn Robber, Thorn Thief and Thorn Usurper and my count jumped to 349, so those are definitely off in the bind file, and I checked Annihilator by hand as well and now my badge count is at 350, as it should be. So those particular badges are still off in the most recent compilation of bind files.
Physician, Mercenary and Trouble Maker Day Job badges on her appear not to be causing her count to go awry. So her count seems to be not over what it should be at least right now.
That was all done with HS.
Frustratingly enough, HS is refusing to detect my blueside badge char, Cry of Muninn so I'm running just Glycerine now and the bind files to test her.
...more frustraingly, Glycerine seemed to detect her when I initially signed onto her as she is now in my CIT profile, but I Just ran through the bind files on her and Glycerine is showing me as Offline. However, it does have all the badges I just went through in the Badges Pending list with none in the Badges Sent list...
Argh.