What Alan meant was that one easy mistake to make is thinking you're downloading your new .out file whenever you push the Deploy button.
There are different .out files from each project.
That's only true if you remembered to select the newest one in:
Window->Preferences
FIRST Downloader Preferences
and check to see that the .out file selected is the latest one AND the directory is the right one.
I always double-check by looking at the .out file creation date in Windows Explorer to make sure it is the one being changed whenever you compile.