Today there are widespread reports of skill queues being paused and even wiped.
It currently seems to be random whether your account has paused or not, and it seems to affect Alphas and Omegas. Subbed and Plexed accounts are affected.
There are several working theories about the implementation. One of which is that if your queue is longer than your remaining sub time, your queue was paused or wiped.
Our recommendation is that you should login and check your account, regardless of the status. At present, there is no official word from CCP, but we will keep you updated with any developments.
Update: It seems that queues are pausing even after being restarted as well, so keep an eye on your accounts.
Update: a GM has posted on EVE-O to say they are investigating
Update: CCP says the problem is fixed.
Final Update: CCP Falcon has confirmed it is related to Ghost Training in this community announcement.