We noticed recently that if you select a range of bookmarks in the Bookmark Manager and delete them, something funny happens: they don't disappear! In many ways, they seem to be gone; you can't actually access them, for instance, but they look no different from ordinary bookmarks. If you restart Firefox, the deleted bookmarks really do go away.
We filed a bug against Firefox for this, and it was recently identified as a duplicate of another bug that was filed last week. So at least we're not the only ones that have seen this. Whatever the problem is, it doesn't seem like it's caused by or related to Foxmarks. But we thought you should know anyway.