There could be issues going on that I don't know about as I have never had a bitch in whelp (there are quite enough unwanted dogs out there already - thank you!!) - however - I have had a heap of fosters thru my home that have either never been house dogs, or have become used to the pound routine, where if you gotta go - you just go.
I simply make sure that mine are taken outside regularly, and supervised!
Not just by opening the door and leaving them to their own devices - but by watching to see that they relieve themselves and they are praised when they do.
In the early stages, this means taking them out - whenever they get up from a 'rest/sleep time' - after they have eaten - and certainly every couple of hours during the day/eveining - last thing at night before bed - and yes with boots and raincoat on if necessary.
I expect, and get a few mistakes, but within a relatively short period of time, the desired result is apparent - but it takes time, patience and consistency.
And I NEVER chastise a dog that has soiled in the wrong place - it is my fault for getting the timing wrong!!! ( I may curse to myself - but never chastise!!)