I am in the same boat as the OP.
I have attempted to apply for the ETA three times.
Credit card charge goes through. No email confirmation, no ETA approval, no way to follow up.

I know of the "leniency period" being granted for ETA applications.

My question is - do the airlines know this too?
The last thing I would want is to show up at the airport and find out that an ETA is required!

My corporate travel agent tells me not to worry.
My instinct tells me the airline check in agents are not to be trusted...