It has worked this way for a while. Notice that the two URLs you link are not the same. One is showing ALL posts tagged "Gannons Bookmarks" and the other is showing ONLY posts tagged "Gannons Bookmarks" and made by user GannonNotFromZelda. The "all posts" feed ignores reblog-with-comment and the "user only" feed includes it.
If you have identified something that changed with the recent changes, it must have been that some link somewhere switched from linking the user-only search to linking the all-users search.
GannonNotFromZelda