I thought filtering was to do with downstream.
No, filtering is intended to separate the telephone frequencies (up to 4 kHz) from the ADSL frequencies (above 25 kHz). The ADSL frequencies starting at ~25 kHz are the upstream ones, and these are the frequencies which are more likely to be affected by imperfect filtering.
As to the culprits, there's large range of possibilities. Normally the first thing to do is to connect the router to the test socket inside the master socket, to eliminate the internal wiring. But if I understand you correctly, your extensions are directly wired to the back of the socket and not into an NTE5 faceplate. If you haven't got an NTE5 then the best technical option would be to get an NTE5 fitted by BT.
That being said, it may not be worth the bother. If your connection is stable and adequately fast, the variation in upstream SNR margin is really of no consequence, so the best thing to do may be nothing.