Issue with assistive access not keeping permissions

Question

Since a recent upgrade (likely from OS X 10.9.x to 10.10.2) I've had issues with Assistive Access blocking Automator and Applescript from interaction with dialogs.
If I run my script or my Automator workflow (which basically has the same script in it) I get the error:
System Events got an error: Automator is not allowed assistive access. (in the case of Automator).
If I open Automator, and then untick and retick the Automator entry in the Accessibility options within Security & Privacy (System Preferences), then workflow can run again. It continues to work until I Quit Automator. Then it's as if OS X no longer trusts Automator to be the same app I gave Accessibility permissions to.  And the situation repeats. It's much as if it were not code-signed. The exact same issue plays out with Apple Script.
I came across this info, which I hoped would solve the problem, but it made no difference: http://macscripter.net/viewtopic.php?id=43394 and http://bit.ly/1x3SRmc
In my Accessibility permissions I now have:
Script Editor
Automator
1Password 5 (which the script interacts with)
com.apple.security.agentStub.xpc (in case that's being called up and triggering the Accessibility issue)
osascript (in case that's handling the script and triggering the Accessibility issue)
SecurityAgent.xpc (in case that was triggering the Accessibility issue)
I added all these because the post at http://bit.ly/1x3SRmc     indicated that anything Apple Script is interacting with needs Accessibility access permissions.
My script is as follows:
set appName to "SecurityAgent"
set passApp to "1Password 5" (* set this to the name of your password manager *)
tell application "System Events"
  if not (exists window 1 of process appName) then -- test if SecurityAgent window exists
  set answer to display dialog "The password dialog was not found. Please check." buttons {"Ok"}
  return -- abort if SecurityAgent window does not exist
  end if
end tell
tell application "System Events"
  set position of window 1 of process appName to {10, 10}
-- move SecurityAgent window out of the way
end tell
activate application passApp
tell application "System Events"
  tell application "SystemUIServer"
  set answer to display dialog "Make sure correct 1Password item is actively selected (i.e. click it again if it was previously selected), then click “Continue” to proceed." buttons {"Continue"}
  end tell
  tell process passApp
  (* If you are not using 1Password, you may need to change the menu item clicks, below, to whatever is correct in your particular password manager *)
  click menu item "copy password" of menu "item" of menu bar 1
  delay 1
  set appData to the clipboard
  end tell
  tell application "System Events"
  tell process appName
  set value of text field 1 of window 1 to appData
  if exists (text field 2 of window 1) then
  set value of text field 2 of window 1 to appData
  if exists checkbox 1 of window 1 then
  if value of checkbox 1 of window 1 is 1 then
  click checkbox 1 of window 1
  end if
  end if
  set value of checkbox 1 of window 1 to 0
  delay 1 (* gives  a moment to see what's going on *)
  click button "OK" of window 1
  else
  if value of checkbox 1 of window 1 is 1 then
  click checkbox 1 of window 1
  end if
  delay 1 (* gives  a moment to see what's going on *)
  click button "OK" of window 1
  end if
  end tell
  end tell
end tell
In Automator it would appear the script is generating an error as soon as it reaches line 5, "if not (exists window 1 of process appName) then"
I would greatly appreciate some assistance in resolving this issue.

Answer 1

Starting with Mavericks, Apple changed the way that the accessibility works (see Using AppleScript with Accessibility and Security features in Mavericks) - each individual application needs to be given access, instead of a global option.  A regular AppleScript application saves properties and global variables with the script, which makes it a new application as far as the system security is concerned, so it needs to be re-added to the accessibility list.  To work with this new security feature, you need to code-sign your AppleScript application or make the script(s) in the bundle read-only so that they don't get changed (note that an AppleScript-based project in Xcode does not modify the application bundle by saving properties and globals).