Ok, I'm not sure if you're still taking bug reports for Book I or not but, if you can figure out why this happens, maybe you can prevent it in Book II.
Anyway, there is only one place in the whole game where it is always safe to rest and spend the night - the Owl's Roost Tavern in Aridell run by Porter. In a game I was recently playing, about midway through the game (I was at the point where I was trying to get into Crakmir through the Ossuary), I went in to the tavern for the night. I went into the bedroom where you wake up in order to talk to Porter, who had wandered into there. I paid my money and woke up in the morning. Porter was still in the room. I walked over to the cabinet where I was storing stuff to swap inventory around. Porter attacked me!
I reloaded the game from the night before, and tried it again. I happened again. I then left without swapping around inventory and went on adventuring. A few games days later, I came back to the inn. This time Porter wasn't in the room. I sold him some items, then bought the room for the night. When I woke up in the morning, Porter was still in the outer room. I went into the cabinet to swap inventory again. When I came out of the bedroom, Porter attacked! At that point, I was forced to kill him so I spent the rest of the game without a safe place to sleep and recover hit points/mana.
I don't know why Porter suddenly went hostile while I was rummaging around in my own stuff. The other townsfolk were not hostile. And, it only happened this game and not in any of the others I've played. I wasn't wearing the Evil Amulet, or any item marked as "Evil". I did not attack Porter first. I also didn't see a message in the text area about Porter hearing a crime being committed as if I had robbed a chest. I can't think of what I did that might have caused Porter to become hostile except open the chest that I've opened dozens of times previously in the game, and moved my own possessions around between the drawers and my pack.
Just thought you might want to know. It's really not fun to lose your only truly safe haven. Hopefully, this won't happen in Book II.
BTW, I'm playing on a Mac, OS 10.4.11. i don't know the version number of Eschalon (there doesn't seem to be an easy way to find out, even Info in the Finder doesn't say) but the date on it is Dec. 2007.
Hope this helps...