I've seen that kind of problem on an earlier model of MSR filter. Have you looked at the foam filter on the intake?
Years ago we had some really ickky raw water as our only water source, so we pumped it. After about one quart, the progress slowed down to nothing. We fooled with it, cleaned it, poured boiling water through it, and everything else, and it was still clogged somehow. This particular model had a top metal screen, a ceramic filter, and then a paper filter. We had to quit using it and boil our water, instead. After the trip, I took it apart and tried a few things. Once the paper element was removed, it worked perfectly. Why would that matter so much? Because the raw water had something oily in it, and that coated and blocked the paper element pores. Had we known, we could have simply removed the paper filter on the trip.
Your filter is not that complicated, but it might be something similarly easy to fix, like with the foam filter piece.