When I visited our site on my phone and used the “Real Time / Locations” tool in GA, Vancouver did not appear on the map. Other cities were, but not Vancouver at all. I did a quick test on my desktop browser and North Vancouver popped up right away.

Assuming this is an issue with the Mobile Joomla extension, I looked into the documentation. There’s mention there of some extensions that need to be added for mobile tracking.
Those details are here: www.mobilejoomla.com/documentation/14-extensions/65-google-analytics-mobile.html

I can’t find these set up in our Admin area, so I’m assuming this extension is not installed, and so I’m guessing there is no GA code on my phone as I browse the site. So, I’m wondering if Mobile Joomla is not counting visits from phones, or at least, iPhones like mine?

There is some confusion because the GA is counting “mobile” visits, so somehow, we need to assume that not all mobile traffic is not being counted. The “mobile” visits corresponds roughly to what I’m reading out there about how many people visit web sites on mobile vs. computer.