The solution to the problem is very simple. More and more frequent saddle time. The problem is that the tissues which you are compacting lose blood flow during said compaction. The lowered blood flow causes the pain. That's normal and not worrisome as long as it's just the tissues over your sit bones. In time, those tissues will respond to your abuse by becoming tolerant of decreased blood flow. You can speed up the process by riding some every day, if only for 30 minutes. More frequent riding helps more than longer rides. Increase the length of your long rides as your tissues become more tolerant. A different saddle may help or it may not.