I have quite a lot of filters in place in Kmail. As of late those filters are not filtering incoming mail anymore - which they did until recently - and aren't applied when I press "Apply all filter on this folder". When I go into the filter settings and press "apply now" manually it does work. What is wrong.

I have KDE 4.13.3 on Kubuntu 14.4.

This is a very old version of PIM that is not actively maintained anymore. You may want to check if newer versions (using a liveCD or something of the sort) still exhibit the issue with simple filters and some test mails.

That is a little unfortunate. It's on a LTS after all...
Also, it worked until rather recently.

I found that this seems to be a bug that exists since 2010... and is also confirmed recently:
https://bugs.kde.org/show_bug.cgi?id=255388
How is that even possible? How come this is not been fixed...?

Strangely enough this only goes for my mail in the inbox. The filter for my outbox (which is to move my out-going mail into the inbox) does work!