Zend certified PHP/Magento developer

Why are some emails marked read and others unread on arrival using IMAP in Thunderbird?

On advice of my provider, I recently switched to IMAP on my desktop but left POP3 on my phone and elsewhere. Incoming email seems to randomly switch from read to unread when it appears on my desktop. That is, if 100 emails arrive at the same time, a third may appear read and the rest unread. And they may be mixed up.
To further complicate things my mail is filtered on arrival through junk and then into some two dozen folders.

I often get as many as a thousand emails a day or more. Keeping read and unread status clear is essential for my sanity.

How can I solve the problem?