Something doesn't make sense with what the agent said, I think she is only partially right (right that you can upgrade, wrong about when). IMHO you should try to use your eUpgrades at the regular E50 upgrade window for Flex.
Click on "sun destinations" using the following link:
http://www.aircanada.com/en/aeroplan...des/howto.html
The booking window of "at check-in" (i.e. within 24 hours) only applies for booking classes G, A, W, S, T, L and K. If you are on a Flex fare, your regular booking window should apply. Repeating what I stated in my previous post, the only thing that is special about ACV bookings is that SE100's and E75's have an additional benefit over other elites where they can upgrade from Tango fares (since you're not on a Tango fare, the associated requirements should not apply).
Please report back about when you're actually able to request your upgrade.