Conversation Conundrums

Spent a lot of time over the weekend working on the module. I finished up two more areas, wrote two new, relatively short conversations, and finished up a lot of other things. I ran into a big stumbling block when I tested the Bertram conversation. When the PC first talks to him, there are four responses to his initial greeting. I found that, depending on which one I chose, sometimes the conversation would go the way it should, but other times it would play out as if the PC had a certain variable on him that he shouldn't have. After asking around, I thought what had happened is that I had made some bad links from the original conversation node to the node that only appears when that variable is set. However, after painstakingly testing out all the conversation options, I discovered that, in fact, the conversation was beginning on the wrong node, and that that node had some bad links to the original one. As it turned out, the problem was with the item OnAcquire script. I tried to write it so that when the PC picked up item A when they had variable B set to 1, then it would set the variable to 2, but if they didn't have that variable set to 1, it would set it to 3 instead. However, the way I structured it, it was setting variable B to 3 on all my items when the game started (I didn't know that script always fired at the start of the game). Someone on the forum rewrote it for me, and it works now, although when I first tried it something very weird happened: all the NPC's began attacking each other! I have absolutely no idea how this happened, because the script that was changed had nothing in it that would make the NPCs attack each other. I went in and discovered that the "dead" NPCs were in a different faction than the living ones, and once I changed that things were fine, although even so, I still don't know why they attacked each other because A) The two factions were friendly to each other and B) There was nothing that should have set them against each other. All I can think of is that at one point the toolkit didn't shut down properly, so maybe that caused some temporary weirdness.