I was having the same problem and this is what worked for me:
Open your CHART OF ACCOUNTS; right click & choose the option to customize columns in the COA.
Add "1099 Account" to your display & you can see which accounts are associated with it.
Go to VENDORS at the top toolbar, then down to PRINT/FILE 1099's, then to 1099 WIZARD .
Go all the way through the wizard, (even with nothing to file for 1099's), until it is completed / finished.
Go back and look at the 1099 boxes next to the COA - mine all went away.
Now I can arrange / change as I need to.
