Instead of using a period to separate the month from the day and the year from the month, try using a space.
I can make this change if it's the only way, but I was previously able to use the naming convention described. Now due to some arbitrary change made in an update to Lightroom it will no longer be consistent with numerous catalogs that I've already been using this convention and if I do as you suggest the new folders will not be in sequence with all of the other folders.
My suggestion was for you to simply try an experiment doing this, so that we could determine if the period was the cause of this problem, or not.
To my knowledge LR does not control characters you can and can't use in either folder or file names. That is left up to the operating system you are using, which you haven't bothered stating.
What OS are you using?
Your naming has 2 periods in it. A period is usually used to separate a File Name from the extension. Are you sure you used a space after the last numerical date entry before the - in previous folder naming? Have you tried 2016.12.09-Title to see if that get created correctly?