I had this problem with the disk version as well; I'll talk to one of the NPC's in town and they suddenly turn hostile and attack me. I don't have any negative modifiers and my town rep is fine. It happens in Tarant at Madam Lil's, the Gnome that's kicking the dog in Ashbury and the firearms master trainer in Ashbury. The only thing I can think of is the unofficial patch as it's the only commonality between the disk version I played and the Gog one I just purchased. It's the 91225 version.

Maybe it something you said to them that they didn't like.
I don't know about the Madam, but i know that at least one dialog leads to combat with the Dog kicking gnome, and the same thing is true with the firearms master.

Other possibilities:
Maybe your character is a combination of race, beauty and charisma that sets peoples' teeth on edge and unfortunately generates, through dialogue, a loop of events where they become less and less able to stand you until they irrationally decide to kill you.
What is your race and build?

Try wearing a Smoking Jacket or that particularly formal dress. Expensive, but worth it regardless of your troubles, and doubly so if it makes things work right for you now.

Alternatively, somebody else on here had a similar problem but only in Tarant. If there's no reason in your race and build to think there's an issue, and if the smoking jacket doesn't help, see if you have the same problem in other towns. If not, that would be useful to know.

I'm playing as a tech based human. At Madam Lil's I opened the dialog and everything was fine. The next thing I asked was something like "what do you do here?" I've played the game years ago and was never attacked by her before. All my stats are at least 10 because I don't want any negative modifiers.

I'm less surprised and amused by the presence of a bug (in Arcanum?!) than by the narrative it produces.
That said, believe it or not the smoking jacket may help. It changes the Reaction modifier, which has much to do with who attacks you when. It may cause it to think twice about how its NPCs react to you. At the least, it might help for debugging purposes.
And again, you might check to see if it's only a problem in Tarant, or for that matter only with Madam Lil.

I'll try the jacket and see if that works. I'm going on the assumption that other areas are bugged as well though I haven't tried them yet.

There was recently a similar thread on this topic, and the OP concluded that it was a bug resulting from TOO HIGH reaction. He claimed that wearing dread armor (to lower reaction) solved it.

A second possibility--I had a bug where, after accidentally attacking someone I should not have attacked and then reloading a saved game, the character would turn hostile as soon as I spoke to him. Only way I got around it was starting a new game.

Surely there's some kind of save-hacking you could do?

Has your character stolen anything in any of those towns recently? Failed theft can cause entire towns to go hostile on you for up to a month of in game time. A lot of times if you simply leave, then visit other areas, the hostility will be reset. Note, some NPC's have relations to other NPC's that if you have killed will make it so they still hold a vendetta against you, so for if example, one of Madame Lil's quest subjects end up dead, potentially a good share of Tarant could and will end up hostile.

I tried the smoking jacket and same thing. I haven't stolen or even attempted to steal anything in town. Madam Lil attacks me first time I enter her store and start to speak to her. I'm going to try the other end and try wearing dread armor.