... As Jack said, by jiggling the chain, you may 'lift' it out of the drain which is probably why the flapper isn't sitting completely shut. Or, the handle 'bar' is tapping something just enough to stop the water. If the bar happens to tap the float (which is REALLY way out on a limb), it may cause the float to rise 1/8" and cause the water to shut off.
Take off the lid and look inside while the water is running. Look at the chain. If it's OK, look at the overflow. If water isn't running into it, look at the float. At SOME point, jiggle the handle to see if the 'err' is corrected.
My best to ya and hope this helps.
Jay J -Moderator
PS: If the chain is the culprit, take up just enough slack so that it won't interfere w/the drain. Don't take up more chain than necessary. (I think we earned our $$$ on this one ...)