You problem is probably because of the new Hotmail interface involving the
"focused Inbox" messages option Hotmail has instituted. None of my 10 Hotmail accounts have been updated to this new interface, but I understand that if this "focused Inbox" filter is enabled then some users have had issues with POP Peeper retrieving Hotmail messages.
You are presumably using the
Webmail protocol, that is to say that your "
Server type" is set to "
Hotmail/Outlook" in your POP Peeper Hotmail accounts.
If this is correct (which I assume to be the case) then by switching your Hotmail accounts" to
IMAP ("Server type" = "IMAP") in POP Peeper you should find this problem with POP Peeper will be resolved.
Alternately if you want to continue to use the Webmail protocol then you will need to disable this feature in your Hotmail account on the web by clicking on "
Filter" to
disable the "
show focused inbox" option or alternatively accomplish the same thing as illustrated below using the accounts "
Options" page (refer to screen-shot below, click to enlarge for better readability).
This is because POP Peeper does not currently support the Hotmail filtered inboxes via the webmail protocol that the new Hotmail interface uses.

- Examples of how to turn off the Hotmail accounts "focused Inbox" filter.
(allowing the continued use of Webmail protocol)
Good judgment comes from experience and a lot of that comes from bad judgment. - Will Rogers