I seem to have approximately the same problem with a similar AppleScript. But this is related to an Alfred Workflow. (Hotkey + Launch File Action.)
The entire AppleScript contents are added below.
When I run the script from the Script Editor, it opens two Finder windows and set the proper bounds and positions. As expected.
With Alfred 3, however, it runs the script twice. It didn't occur with Alfred 2.
Running:
Alfred version: 3.0 [645]
OS X 10.11.5 (15F34)
Otherwise, I agree: Alfred 3 is an utterly great product!
Best regards,
Hans Trygve Jensen
======= The Script: ======
tell application "Finder"
activate
-- Uppermost window
make new Finder window
select Finder window 1
set current view of window 1 to column view
set toolbar visible of window 1 to true
set sidebar width of the front Finder window to 172
set target of front Finder window to home
set position of Finder window 1 to {1, 44}
select Finder window 1
set bounds of Finder window 1 to {1, 22, 1100, 440}
--Bottommost window
make new Finder window
select Finder window 1
set current view of window 1 to column view
set toolbar visible of window 1 to true
set sidebar width of the front Finder window to 172
set target of front Finder window to startup disk
set position of Finder window 1 to {1, 464}
select Finder window 1
set bounds of Finder window 1 to {1, 442, 1100, 860}
end tell
