[imported_Jiraiya]

From my experience if there is a variation in the item quality or color or anything else, they wont stack together. So you cant put 1 exceptional bandana on a stack of non and sell them all as exceptional. Doesnt work like that.

edit: sorry I just noticed a few bits in your post when i scrolled up that I didnt see before:

1) If the first item I make is not exceptional and all items I make after the first are exceptional and add onto the first one, they will all sell as not exceptional.
2) If the first item I make is exceptional and all items I make after the first are not exceptional and add onto the first one, they will all sell as exceptional (this is the opposite of number 1).
3) Items made from different materials stack. I made a copper dagger then an iron dagger and the iron dagger stacked on top of the copper dagger.
4) I made 3 exceptional daggers in a row and one non exceptional dagger and placed them on the ground as I made each one so they wouldn't stack. I picked them all up and when I went to sell them I had 4 items in the sell list; 3 x 1 dagger at 12gp and 1 x 1 dagger at 10gp. I then stacked the items ontop of each other and said sell again. Now I had 1 item in the list as 4 x 1 dagger at 12gp (my not exceptional became exceptional). I then unstacked the items, said sell again and now i had 4 items in the sell list; 3 x 1 dagger at 10gp and 1 x 1 dagger and 12gp > it's the reverse of before I stacked them!

Your absolutely right that is most definitely a bug. They shouldnt be doing that. Which version of the tiledata.mul are you using? I'm not sure if it matters but it might be helpful to the devs when debugging this.