Thanks for the offer of help Chris.
Detailed reports of the various issues are most helpful.
We have about 60 sites which we monitor in WP Remote and we haven’t seen any issues with plugin updates not showing etc.
With those the issue is likely either the specific plugin, so if you have a specific plugin which is refusing to show an update, let us know so we can test with that specific plugin.
If it’s not just a specific plugin, a detailed as possible report on when the updates don’t show.
There are some scenarios where a plugin update will be visible on the site but not through WP Remote. For example if you refresh the site on WP Remote, it hits your site and does an update check, that says there are no updates, later you visit your site directly and that triggers another update check, this time there are plugin updates. For those plugin updates to show in WP Remote you would need to refresh the site in WP Remote so that it then goes back to your site and gets the latest status.