Sounds really odd, you should probably get in contact with support.

If you waited 'til your build time for the upgrade + the time needed to generate the youths would add up to the 2nd day of the season after then I don't see how it couldn't work. Re-do your maths and make sure, at different levels the time needed to generate the youths is shortened so that might be why you're not getting time into the following season.

If it's not your maths that's the problem then it's likely a bug.