As a service plumber for years, I have seen this intermittent problem for years among all sorts of toilets. The more difficult to repair are the simple newer chain activated flappers, mostly because the problem can be so intermittent, even rare. Even when some of the typical issues are solved (chain too long and getting under flapper, chain too long and catching on lower link at the s-hook), there are issues where a cheap type twisted wire chain (the ones where links are created two at a time by twisting a short wire) is cut to the optimum length but has one double link turn at just the right angle to hang up at 90 degrees, effectively shortening the chain. This is one of those things that happens maybe every 50 or 100 times; usually as one flushes as one leaves for the day (thus leaving the toilet running all day), or a 3 am when one really doesn't want to make a second trip to the john. In my own home I have found only a few, not always perfect, solutions. The main thing is to be willing to put in enough time and enough care to carefully adjust things, especially as one is often working on the problem at 2 am and know a quick, easy fix will get you through for a while..
One solution is the use of good beaded chain, an item that was once in common use. The problem is to make sure you get this made of a material suitable for use in your home's water that won't degrade in a year or so. The other problem is finding chain to hook adapters for either end. But, when cut to the right length and with proper adapters, I've seen toilets that operated trouble free for decades. The other is to use real chain, even plastic chain, avoiding the double link type. It is also a good idea to take one's time cutting the chain just right (a good idea to buy about three time the length you may use as it's cheap and you may cut it too short) and bending any attaching hooks so they can't hang up on the chain.