"Comcast custom folders" means folders you are creating up on the mail
server using the webmail interface to your account (i.e.,
http://www.comcast.net/qry/goto?app=mail). Or did you create these
folders within *Outlook*? Since you're talking about sorting (by
category) and since Comcast provides no server-side rules that you can
define, I have to assume you are using rules in Outlook to move mails
into folders defined in Outlook based on a category that has been
assigned to those mails.
Rules only fire *automatically* when the mails are received (i.e., when
they go into the Inbox folder). Rules are only exercised against mails
in the Inbox folder by default. If you manually exercise the rules, the
items need to be in the Inbox folder UNLESS you select a different
parent folder from which to start exercising the rules. I don't have
Outlook on my new-built host but, as I recall, and when exercising the
rules manually, you had to select which folder on which to run the
selected rules. The default is the Inbox folder. Pick a different
folder when you manually run your rules. Again, automatic execution of
rules only is against mails in the Inbox folder.