Sometimes I'll try to apply an effect to a long clip and it only applies the effect for the beginning of the clip, and then it just cuts off, it happens with every effect
Which version of Kdenlive and MLT are you using? Which version of Ubuntu? Have you tried using our PPA's?
I'm having the same issue. I was using 4.16.12.3 on Ubuntu 17.04, but I installed the version from the PPA (4.17.04.0) as you suggested: same result!