It's most probably just a timing issue. PF3 doesn't control AI traffic and only simulates ATC instructions to AI aircraft on an 'after the event' process. eg. Let's say during a sweep of AI modes we detect an aircraft that is taxiing out. During the next sweep we find that same aircraft is in 'taking off' mode, at which point you will hear PF3 ATC giving them takeoff clearance. But of course they 'could' be at the point of rotating, in which case it wold not look very realistic. We also only provide ATC for to AI aircraft consecutively, then PF3 resumes other processing, like ATC talking to you perhaps. Otherwise PF3 could get caught up doing nothing but chatting with AI aircraft at a busy airport.
Unfortunately it's almost impossible for me to determine exactly why you're not hearing ATC giving takeoff clearance but I would doubt it's stopped working completely and is probably just one of those things.
If it is occurring frequently then please attach your debug log, just so I can see if you have any other issues that could be causing this problem.