Do you bubble CO2 into, or anywhere near the intake? If so be sure to remove or turn off the CO2 before turning off the filter to pull it for servicing.
I've found it far easier to get running again if I use the method prescribed in the manual and do not add any water back into the canister before connecting the tubing. Your tubing should still have water inside it and when you push the locking valve down this will automatically start the water draining from the tank to fill the canister to the proper levels.
I know, I've tried to cheat and just fill the canister because I don't want to have to then top off the tank. Now I just give in, clean the filter, replace and prime the filter, and then add two gallons of water to the tank.