In case you missed it on the Tapspace forum, here's my response from there:
Quote from: KevinShah
I did start with a brand new sib 7 template - totally from scratch. The only thing that I did that may have changed it is import my own house style...would that do it?
Yes, that could definitely do it. If Sibelius sees that there are differences between noteheads lists, it will try to compensate for it. The end result can be added notes to the noteheads list, and then corrupted mappings. Since you're getting the "strange" noteheads during input, this seems the likely culprit.
What elements are you trying to import into the template?