Jenny is supposed to get more in version 0.18.5, including bed crawl scenes.
If you are not submissive to her (i.e. don't stay silent during arguments, don't give her the money straight away) she will not be such a bitch.
If you mean Diane's drink and Harold's donut orders are different than before: they are random each time as far as I know. Was so since ever.
I had the pom pom search, Roxxy met Jenny. I guess you are right, seems to be related to the bug that Jenny did not take the money.
I had no problems catching Aqua. You sure you talked to Cpt. Perry before, chose the right bait, and hit the right spot?
You mention the house tree scene -- I remember there was something, but I did not get it. Maybe I will start the game right now and see what I missed