" I didn't realize that that login was for ancestry.com"
All the different country urls link back to the Salt Lake City set of servers so it doesn't matter where you are.
When FTM has to connect to Ancestry to search it always uses Ancestry.com which is the site you register with when you activate.
The website format you see is based on your profile and the country version of FTM. I'm in the UK and FTM always searches on Ancestry.com but it restricts me to UK databases based on my subscription.
If I log in outside FTM, via Firefox to Ancestry.co.uk, I have to sign in separately and get the id and password saved in that browser. If your default browser isn't IE then you may not be able to login automatically without first signing in separately.
It's all done by cookies, If the cookies disappear then the login id disappears. Or so it seems.
If your problem is that you can't search via the .ca url then you'll have to sign in separately and get it to remember your id and password.