That sounds like an unusual fault for sure and i am not sure i can offer anything other than more speculation,but with my knowledge of electronics and thinking about it-
-The graphics may be breaking down when the cd drive is trying to read a certain area of the disc but the problem would happen with all games so that is unlikely.
-Usually graphics breaking up after a period of time is due to a either thermal problem or slight voltage change (instability),capacitors are used to filter and regulate and so are prime candidates for this problem and may others but again would this not happen with all games?
-Maybe the Ecco games use a certain area of ram or other i.c that is not used by the other games,and this ram/i.c could be faulty?
I will have a look on the net and other forums like Sega 16 for other similar problems and solutions.