In Scrivener 220.127.116.11 changing the order of meta-data in “Edit Custom Meta-Data Settings” (using the up/down arrows) changes the columns selected in View >> Outliner Columns.
This is a known current limitation, not new to 1.9. There is an info message about it that appears when you change the order in the meta-data pane, so my guess is that at some time past you got this and checked the option not to show the message again. You can reset all such messages via the “Reset All Warnings” button at the bottom of the General tab of Tools > Options.
After you’ve re-ordered your custom meta-data, you reset the columns you want via View > Outliner Columns, and drag and drop the column headers to rearrange them in the outliner.