Thanks. Not the flexible hose below canister (I have cleaned a lot of them!). Also, seems to not be the filter, I washed that thoroughly to start with.
So I tried a DC54 canister on the DC39 - good suction, no pulsing. Then tried the DC39 canister on the DC54 - worked with no pulsing. BUT the DC39 with DC39 canister still pulses. I might have to disassemble the DC39 canister.