We have approx. 500 collections with update schedules running pretty evenly throughout the day. As I'm sure you will agree the annoyance of the the old Update Collection Membership and then refresh the console is a blight on our day - but when that little red eggtimer WILL NOT DISAPPEAR it sends my SCCM OCD twitching and I just cannot carry on with my day until I've sorted it...
It seems the actual problem here was down to the sheer volume of collections running updates. There was a cumulative effect of the schedules and come 1pm the collection action list was backed up with about 3 hours of updates pending.
I've gone through and removed all update schedules from our collections (yes - it was a lengthy monotonous task) and all is well.