Part of the queue issue is that, as I understand it capacity in the Cathedral is still limited to 225 persons. The security staff keep careful counts of people entering through the two doors - Holy Door and South Transept (Plaza Praterias) and exiting via the North Transept (Plaza Inmaculada).
So, when there is a Mass occurring, the queue at the Holy Door should necessarily stop for about 45 minutes. Once Mass goers leave, a like number of worshippers can be allowed in.
This will likely continue until the capacity restrictions are raised or removed.
If this changed recently and I missed it, please correct me.
Hope this helps,
Tom