There is a bug that has crept into the current version regarding this. (See this thread, or this thread, for example) The method of assigning the time sig really shouldn’t matter at all, but apparently it currently does.
If you use the Hub or the right panel to assign the time sig, it seems like there are some Notation Options baked into the meter that won’t update if you make changes to them. The safest way to make sure your Notation Options are being respected seems to be deleting any existing time sigs that weren’t created with the popover, and re-inputting them using the popover.
Hopefully the devs will get this sorted out soon as the grouping options are causing daily posts on the FB groups too. Some of those are ex-Finale users who don’t understand the options, but some are a result of the options not actually being correctly applied. New users are obviously more likely to input time sigs from the Hub or the right panel as they are still learning all the popovers.