Automator finish one task before moving on?
Unfortunately empty trash is a message sent to Finder, and, from Automator's point of view, the task finishes when the message is sent.

In this conversation there's a possible solution. You have to modify your Applescript task with a check on the size of the trash:

tell application "Finder"
    set first_size to ""
    set second_size to " "
    set trash_folder to (path to trash folder)

    empty trash

    repeat until first_size is equal to second_size
        set first_size to size of (info for trash_folder) as integer
        delay 2
        set second_size to size of (info for trash_folder) as integer
    end repeat
end tell


This way the task will not end until the size of the trash stops decreasing.

If you use tmutil for time machine backup terminal command, there is a -b option for startbackup command that tells the script to wait until the backup is finished before exiting.