The problem you are encountering is that you are not assigning the radio buttons to a variable. The easiest way to do this is with Assign and Eval (listed in the help file). Another way is to add a column to your $aArray and assign the radio button to the 2nd column of the array when the radio is created. This method is just as good, but will make you re-work all your $aArray reads.
Anyways, I guess you will choose Assign/Eval, so this will be a good learning experience for you. Assign/Eval are great tools when you are automatically generating lots of buttons, radios, combo boxes, etc.
Basically, when you are creating the radios, it will assign them $Radio1, $Radio2, $Radio3 and you can read them exactly with those variables or you can read them in loops with Eval("Radio" & $ar).
Here's an example where two guis can read the same radio boxes:
#include <Array.au3>
#include <File.au3>
#include <MsgBoxConstants.au3>
#include <GUIConstantsEx.au3>
#include <WindowsConstants.au3>
Global $aArray = _FileListToArrayRec(@ScriptDir, "Setup.vbs||*_bak*", $FLTAR_FILES, $FLTAR_RECUR, $FLTAR_SORT)
$top = 10
$Form1 = GUICreate("Form1", 400, 278, 192, 124)
For $ar = 1 To $aArray[0]
Assign("Radio" & $ar, GUICtrlCreateRadio($aArray[$ar], 10, $top, 350, 20))
$top += 30
Next
GUICtrlSetState($Radio2, $GUI_CHECKED) ; Added this for easier testing
$Button1 = GUICtrlCreateButton("Button1", 264, 208, 75, 25, $WS_GROUP)
GUISetState(@SW_SHOW)
$Form2 = GUICreate("Form2", 300, 293, 700, 218)
$Button2 = GUICtrlCreateButton("read gui #1", 136, 136, 75, 25, $WS_GROUP)
GUISetState(@SW_SHOW)
While 1
$nMsg = GUIGetMsg()
Switch $nMsg
Case $GUI_EVENT_CLOSE
Exit
Case $Button1
For $ar = 1 To $aArray[0]
If GUICtrlRead(Eval("Radio" & $ar)) = $GUI_CHECKED Then ; Use Eval to read the radio
MsgBox(0, "", "Auswahl : " & $aArray[$ar])
$verzeichnis = "C:\scripts\" & $aArray[$ar]
IniWrite(@ScriptDir & "\verzeichnis.ini", "Verzeichnis", "VBS", $verzeichnis)
$verzeichnis = "C:\scripts\" & StringRegExpReplace($aArray[$ar], "\\Setup.vbs", "")
IniWrite(@ScriptDir & "\verzeichnis.ini", "Verzeichnis", "Pfad", $verzeichnis)
EndIf
Next
Case $Button2
For $ar = 1 To $aArray[0]
If GUICtrlRead(Eval("Radio" & $ar)) = $GUI_CHECKED Then ; Same as $Button1
MsgBox(0, "", "Auswahl : " & $aArray[$ar])
$verzeichnis = "C:\scripts\" & $aArray[$ar]
IniWrite(@ScriptDir & "\verzeichnis.ini", "Verzeichnis", "VBS", $verzeichnis)
$verzeichnis = "C:\scripts\" & StringRegExpReplace($aArray[$ar], "\\Setup.vbs", "")
IniWrite(@ScriptDir & "\verzeichnis.ini", "Verzeichnis", "Pfad", $verzeichnis)
EndIf
Next
EndSwitch
WEnd