Basically, this is a problem that was introduced in the development
versions of the Hotmail extension.
It would only tell Thunderbird about the first 50 messages in the
Hotmail Inbox no matter how many were in there when the POP protocol
demands that the server (in this case the Hotmail extension) should
report all messages in the Inbox to Thunderbird. This problem is
corrected in the 1.2.19 release but it means that users who used a
development release and who have inboxes greater than 50 messages on
Hotmail will get all messages (except the first 50) downloaded again.
This is a one time event - after that Thunderbird adn Hotmail will be
in sync again.
The download unread only option is not consistent with the POP
protocol but it can help avoid this re-download but it also has the
following drawbacks:
If you have read a new message on the Web then it will not get
downloaded to Thunderbird (unless you mark it unread again)
You cannot delete messages in Thunderbird and have the message also
deleted on Hotmail (as you can when you do not use "download unread
only") and you must manage the Inbox via the Web interface only.
If you prefer not to use the "download unread only" option then the
main alternative would be to move all messages older than the 50 most
recent messages from the Inbox to a custom folder via the Web
interface of Hotmail. For any user with a large Inbox this makes a
great deal of sense to do periodically since it removes a lot of the
work that the extension has to do in returning the full message list
every time you access your Hotmail account from Thunderbird.