This has happened to me in the past, make sure when you are setting your filter you have everything set correctly to get your full link profile. Make sure you have the inbound links tab selected and your filter is set like this:
Show "all" links from "only external" pages to "pages on this root domain" and "show links ungrouped".
The biggest issue is making sure you have it set to root domain, if not you will only be pulling the backlink profile to your homepage. Let me know if that did the trick, if not i would submit a help ticket to help@semoz.org. They are normally really responsive!
Regards - Kyle