I am still unable to reproduce this (tried with the same setup as you carl_pilk), and also I am finding it hard to work out how it could happen. Update Notifier uses settings saved by WordPress itself to check if a new version is available, so I would have thought that you would also be seeing the yellow update nag in the administration area.
It may be helpful to check what is saved in this setting to get some more information on what is going on. All the info (for core updates) used by Update Notifier is taken from the ‘update_core’ transient. I have a test version update-notifier-menu.php which displays the admin menu with extra info and doesn’t send emails. Just place that in the main plugin directory (along with hello.php – that is Hello Dolly) and activate it (after deactivating the normal version of Update Notifier). The actual code for doing this (if you want to add this yourself instead) is: $current = get_transient('update_core'); print_r( $current );
In the test plugin the (possibly) useful output is under the heading “Contents of update_core transient” at the bottom of the Update Notifier admin menu page.
After doing that you could also try using the development version – link straight to the zip or go to Other Versions on the Update Notifier page – to see if there’s a difference (don’t see what though!)
Sorry I cannot be of more help atm, scratching my head in disbelief mostly ??