I guess your explanation sounds reasonable but we cannot really say whether it is right or wrong. If cic says we have failed to submit our application before ITA expiry, then it is wise to act on the message rather than reading meanings that suit us to cic message which says that our online PR applications have been submitted. I will also try to contact cic today to check if they could provide an explanation for this. In the meantime, I pray your explanation will be right. 
