Check you drivers and display settings. Is CC working?
CC was working fine until 2014. now i have the problem on both. i uninstalled cc 2014 but still get the flickering on cc and 2014.
all drivers are up to date.
i think After effects reloads it self when it flickers.
How recently did you update your GPU drivers? Have you tried rolling back to an earlier version?
I wouldn't expect installing version 13 to have an effect on version 12. They should be independent of each other.