I have the same problem with bar 1 using normal square style. At some point it shifts up by 1-2 pixels, not really sure at which time but fiddeling around with Ace-addon-settings seems to bump it down right again. It looks something like this:
This is caused by oSkin.
I think the option that caused it was the 'mainbar' option.
Use '/oskin mainbar' to disable MainMenuBar support in oSkin. You might need to reloadui to get the bar back down into the correct position.