Mailbox folders look empty but emails show up in search as being in the folders

Mail folders look empty but I know I have filed emails into them. When I search for the missing emails they appear in the search list and show the folder they are filed in and I can open them. Emails within the googlemail white folder appear and the standard mailboxes ie inbox, sent etc are fine. Its just the blue folders I've added. Everything was fine until a few months ago.

I've read posts that say use rebuild for each folder but that hasn't made them appear. I am using snow leopard 10.6.8

Any ideas?