IRCTC : did the quota change in the recent past?

For the last few months whenever I book a ticket through IRCTC I'm always indicated that lower berths are not available. I always get a side upper berth. This happens even when the availability is more than 300. Did the quota for IRCTC bookings change in the recent past?

Another  observation is that IRCTC shows waiting list number when booking. However, on that particular day, there a lots of empty slots in the train. I had booked a ticket for my wife very early, got a confirmed ticket. Few days later when I wanted to book a ticket for myself on the same train, the status was waiting list; I had chosen not to book a ticket because the waiting list number was too high. However, to my surprise on the travel date, I had seen that there were lots of empty seats. Is this waiting list number only for IRCTC reservations? What percentage of the total seats are assigned for IRCTC quota?