I am also having the same problem. I tried the method mentioned above where I had the shower below the purifier - and it worked for about 2 showers - but then it started the 2 second rule again.
EDIT: Added picture. That Dupe is literally skipping away from the shower. You can see his progress bar, and his stats still show he needs to keep showering. But, he'd rather run off and talk about the decor. :-/ Also added a picture showing location of water, purifier, and shower in relation to each other. I had previously had the shower next to the lavatories that were on the floor above the beds.