I use a MJ 1200 and the TLF 150 with about 1/3 of it full of regular capacity GFO. I do find the bottom sponge, which I use, sometimes migrates upwards a bit.
Anytime you stir up your tank or you sump, make sure you turn off your MJ. On occasion I forget to turn it off, then start working in my sump (water change, cleaning equipment, etc.), and the MJ will suck up and deposit all kinds of stuff in your reactor. That will plug it up faster.
Also, how old is your MJ? They will crap out after a while. Just had to replace the 1200 on my biopellet reactor as its output went down to nothing despite multiple cleaning attempts and swapping in a different impeller. It is possible it is due for a replacement and that it isn't producing as much flow as you think.