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Are you sure about that? I can't reproduce your issues. Note:

1) Some perks reset every night (Like "Drunk" / "Playful")

2) There's a scrollbar in the inventory, so when it goes over the border, you can scroll up/ down.

All I know is that I played the game through to almost the end, saved and exited. When I restarted the game and loaded my save all of my progress was gone and Kim was back at her starting place as well as all of Cody's gang in the house and by the mall.