I have configured about 40 filters and I only use 3 POP accounts.
When I fetch new mails, I see the mails coming into my inbox and - most of them - are immediately removed again from the inbox message list as they are moved to different (mailing list) folders. But some of them stay in the inbox which should also be moved.
When I then afterwards select these mails manually and press CTRL+J to manually apply the filters again, they are then moved to the correct destination folder.
- mails should always be moved to the defined destination folders
- mails should not appear in the inbox for a fraction of a second and then moved to the destination afterwards (this is just a graphical glitch, not a functional one)
Fixed in KDE 4.10.1 and later by Wolfgang Rohdewald.