It appears that if you mine a plugged sinkhole, save & quit and re log, and then enter that open sinkhole it will load the first sinkhole that you entered in your world, I don't remember exactly how this happened but i think i went to sw or ham before entering the sinkhole. And i have noticed that if you examine the 'open sinkhole' for some reason the character that you are playing (in my case wickerbottom) is going to say the examination quote for the plugged sinkhole instead of the examination quote of the open sinkhole. And the last new cave I entered it doesn't even displayed the 'generating caves' screen, just the 'loading...' one.
Hope this get fixed soon!
Mine a plugged sinkhole, then save & quit, re log, and then proceed to enter that cave.