There are other reasons why a toilet will run on occasionally. Sometimes there is an issue with the chain, it will get a kink in it or it gets too long and gets caught under the flapper, but with those, if you jiggle the handle, the leaking stops. The plastic jug you put in there can also interfere with the flapper. I would suggest that you remove it and use a brick instead. Use something that is heavy and will stay in place.

If the plumber just replaced the flapper and not the whole assembly, or even in some cases where the whole assembly is replaced, the flapper hinge could have ridden up the overflow pipe. sometimes the flapper is attached tot he overflow pipe with a hole in the rubber, fits like a sleeve and the sleeve might need to be lowered a little.