In your case, you responded quickly to the first offence notice. I would go to the Mississauga Court House on Burnhamthorpe and speak to a front-line ticket clerk about your situation. Make sure you bring the printed proof for the online val tag order; see if they're willing to cancel the second ticket.
If that fails, you'll have to request an 'Early Attendance Meeting' and speak to a prosecutor; worst case, you'll have to plead your story to a Justice of Peace at Trial.
If the ticket was issued by a Private Security Company, it's in your best interest to get in touch with them and tell them you have valid tags to avoid future tickets. If it's City MLEOs then try contacting the 'Parking Enforcement' office and tell them you have valid tags and are waiting for them in the mail.
Maybe even put some information on your dashboard in the interim?
Both tickets won't affect your driver's license, so the only consequence for a non-payment is additional admin fees on your next sticker renewal.