You already said that they are now showing the same updates :P
Have you compared the lists with the latest version of fapman?

If you have installed a package manually, HAM can possibly show an available update for it even though the version numbers are the same (in which case fapman won't show it). If it bothers you, just update it in HAM and stop worrying Also HAM seems to list some updates outside of user/* categories too, are they visible in fapman if you list "all packages (advanced)"?

If there is a real problem (a package is not shown as upgradeable even if one with an actually higher version number is available), then I'd like some more information... Like output of "dpkg --status packagename" for the offending packages and also the exact version numbers HAM lists in the details dialog.