I ended of using 2 separate selectors in 2 different Get Text activities. One for the popup box that has the ConfirmationID without a check box and one for the popup box that has the ConfirmatioID without the checkbox.
1st Selector for popup box without checkbox:
Note: I set the ContinueOnError property to True for this get text
2nd Selector for popup box with checkbox:
I first used an assign activity to set the UploadConfirmation = nothing
I then used a get text activity with the 1st Selector (output value is UploadConfirmation)
I then used an if activity to check if the ConfirmationID was still nothing
If it was = Nothing I then used a get text activity with the 2nd selector (output value is UploadConfirmation)
My workflow looks like this:
NOTE: this worked for 3 yearly report uploads but failed on the 4th. I am busy looking at why. My workflow assumed that the 1st popup was always with no checkbox and then the following ones were always with a checkbox. More testing needed as this assumption may be wrong.