I thought the game is supposed to autosave but I find hen I quit and come back, I am missing new items I have found, it loads up in different spots and I have lost progress?

Is there something I am missing?

As far as I gathered the game only saves when you arrive at a NEW Location, which is somewhat fine in Arcade mode, and rather sucks during a campaign. :/

I have also noticed that the game sometimes creates several numbered save folders (e.g. /0/ and /1/), but always loads the save from folder /0/, although there are later saves created in the other folder.

So if an older save is loaded, try to have a look here:
C:\Users\[user name]\AppData\Roaming\SkyshinesBedlam\Local Store\save\saga1

and copy the up to date file in the folder /0/ and delete the rest. Also delete all log files found under
C:\Users\[user name]\AppData\Roaming\SkyshinesBedlam\Local Store\gamelog

has this been fixed yet?