My alt accounts seem to have a different bag layout than my main account. The backpack seems to be the last bag, and the first and last bag slots are reversed also. The settings between all the accounts are exactly the same from what I can see, ad if I change any of the frame settings things only get worse. Any help is appreciated!

Hopefully the developer can see what I am speaking about from these two screenshots.

SOLUTION FOUND I must have missed a comment on the Curse page of this addon, because I read through them again now and found this:

And this guy is 100% right. I logged on ALL of my older characters that don't have the issue, and they all have the "Reverse Clean Up Bags" setting (The Blizzard one, not the one in Bagnon settings) enabled. Seems like this option isn't enabled on new characters by default! I logged on my new alt and enabled, and ta-da! Everything works just fine like on my other characters!

TLDR; The "issue" is not the addon's fault, it's a WoW setting

I am having the exact same problem as of recently, but only with new alts it seems. On new alts it's like you said, it's like the backpack starts at the bottom/near bottom, so whenever I sort it always starts by stacking items on the second lowest row. And just like you, I have the exact same settings on ALL my characters, yet it only happens to new alts, even if they have the same settings.

I'll upload some screenshots as well. This is one of my older alts, who has been using Bagnon for a few years, when I use the sort function on his bags it looks like this: (as it does on all my older characters)

However on my new alts, it looks like this:

As you can see here it looks like the backpack starts where the hearthstone is, which is on the second-lowest row, and when I press sort, it sorts from where the heartstone is and downwards, until all the rows below are full, then it puts stuff on the row above the hearthstone.

Hopefully this will help in fixing it, because this is an annoying problem that I'd rather not have on my Demon Hunter when Legion comes. :P

EDIT: Forgot to mention that unlike the OP, this issue is happening on the same account, not separate accounts like OP. Also the isse does not seem to affect my bank on new alts, just the inventory.

EDIT2: Random idea, could it have something to do with the size of the inventory/how big your extra bags are? Because I realized all the old characters that aren't affected all have 28 or 30 slot bags, while I give new alts 16 slot bags. I dunno if it has anything to do with the issue, but I thought it was worth mentioning.

I have the exact same problem, however I do not see the:
Game Menu > Interface > Game > Controls "Reverse clean up bags" option.

Yeah this option was removed with the Legion Pre-Expansion patch, like a lot of other interface options. :(

I see, so since this issue is flagged as a game issue, does anyone know a way around it to fix the issue?

Edit: And ask and ye shall receive, here is the fix: /run SetSortBagsRightToLeft(true)