I'm trying to work out if this is something related only to the 'Next unread button' or whether some

I'm trying to work out if this is something related only to the 'Next unread button' or whether something else is conflicting. I presume if you click on the email it is marked as read.. So please tell me if the use of arrows to select emails, still causes the issue.

use of the arrows to select emails has the same result - the mails are not marked as read till I move to the next message

Test if the Sort Order effects the marking of the last unread email. Please select the following Sort Order and tell me if the 'Next unread' button works with a different Sort by order. View > Sort by > Date - Descending - unthreaded

changing to this sort order didn't fix the problem

Do you use the 'Quick Filter Bar' to 'Show only unread messages' - icon looks likea pair of sunglasses? If no. could you please test. Select the 'Show only unread messages' - then use the 'Move to the Next unread mesage' button. Does it still fail to mark the last email as read?

no change in the behavior - only marks a message read after clicking the next unread button

What version of Thunderbird are you using? What OS ? Confirm Pop or imap mail account?

Thunderbird 31.0

Windows 8.1 Enterprise All my email accounts are configured as POP

Please test whether their are any addons causing a conflict: In Thunderbird 'Help > 'REstart with Addons disabled' then use the Next unread button method to see if it works ok. If it works ok then an addon is causing an issue.

I did this and it fixed the problem. I started re-enabling various add-ons and it turns out the problem is being caused when I enable Cloudmark which is an anti-virus add-on.