d0dger,
seems you have some problems here. Let me be up front and say that,
with multiple Hotmail accounts, I am not seeing them. Yes, I know
that does not help you, but it does mean that the extensions can work
well and I would like to try to help - if I can - to get you in the
same position.
First a couple of questions.
You have mentioned multiple downloads and, at the same time, failures
to download.
Can I ask for clarification?
Are the multiple downloads only on the Inbox or both the Inbox and
custom folders?
Are the failures to download only on custom folders?
What options have you selected for your Hotmail account in the Hotmail
extension? Are you using the "download unread emails only"? option.
Hint - best to never do so. Are you switching the "download unread
emails only option". Hint - *never* do so.
Just a bit about downloading emails. These extensions do not *ever*
make the decision which emails to download. That decision is made
solely and completely by Thunderbird itself obeying the rules of the
very inflexible POP3 protocol. However it is based on the information
from the Hotmail server that is supplied by the Hotmail extension
(that is why you must not mess with the Hotmail extension options once
you have set them).
Looking forward to you update.