Wait, I'm confused. I am attempting to get at the problem with sleeping at Penny's, but you are saying there is no problem?
Also, saves from before 0.3.9.5 aren't supposed to be compatible with newer versions. Are you using incompatible saves to play?
Edit: I got to this screen using file 13 and choosing the option "Open the door". What is the problem? I'm able to sleep before and after she goes to bed, no issues. Are you using a mod?
Edit 2: I do see the issue with Lucius' Store. I'll take that to bug reports, kinda surprised it hasn't already been reported. It may be that the one-half isn't supposed to show anymore, but the store shouldn't be open with Lucius not even at the counter, that is odd.
View attachment 1462485