Run vs. Trail Run

Well, either your times were recorded substantially different, or your distances were recorded substantially different, or a combination of both. Without knowing those numbers for each of you, it's impossible to say why the paces were different.

The cause could be:

1. you started and/or stopped recording at different times
2. your GPS settings are different
3. One of you was using 3d speed and/or 3d distance, while the other wasn't
4. Some other factor, such as one of you used a footpod and the other didn't
5. One of you was using autopause, and the other wasn't
6. Any number of other reasons.

We really need more info to be able to answer this

What is "3D distance/3D speed?"  GPS is inherently 3D (that is to say: it measures distance from GPS satellites in 3 spatial dimensions).  Are Garmin watches programmed to discard elevation components to run data?  Is this an option buried in the menus that I'm not aware of?

Garmin calculate the data 2D. If you want it to be 3D you need to enable it in the activity settings. It'll probably add some more distance depending on the grade of the terrain of your activity. But also in activities with changing weather conditions where pressure changes a lot, it may add much more elevation than it should be. Actually, I like and use 3D calculations, however, many people said don't prefer it as it causes wrong data etc...

Most Garmin watches don't use the GPS signal's elevation component, since it's way too inaccurate and noisy. Rather they use the barometric altimeter to estimate elevation changes. To calibrate the altimeter, the watch uses GPS to get 2D coordinates, then consults an internal DEM (Digital Elevation Map) to get an approximate elevation, and calibrates the barometric altimeter based on that. There are settings to decide when this calibration happens and how the barometer is used to measure altitude changes.

The 3D distance/speed setting just decides whether to include measured altitude changes into the distance and pace numbers.

Bitti said:

The 3D distance/speed setting just decides whether to include measured altitude changes into the distance and pace numbers.

Often wondered what "the" generally accepted standard is for this - include or not?

On the one hand, 'not' seems the most pure, and as it's the default I suspect the majority of people use this setting (knowingly or otherwise).

On the other hand, you are indeed running/hiking/whatever the actual 3D distance, and it would be included if a pace wheel was used to measure the course (theoretically - the types of courses where this makes a noticeable difference are likely trails up and down mountains where using a pace wheel would be problematic!). A better example would be cycling a hilly course using a speed sensor, basically the same.

Not sure what the majority of 3rd party mapping / sports-logging sites do (Strava etc) - do they take into account additional distance from vert gain/loss?

Guess it makes little difference provided you stick with a setting - everyone knows their pace will be impacted by elevation change, just with 3D enabled it will appear to have slightly less of an impact. But would help when comparing with others, especially running alongside them, of course along with the myriad of other variables and GPS errors etc.

Suppose to enable it you have to be reasonably confident in your devices elevation performance: with 2D poor elevation performance simply results in poor elevation data, whereas with 3D it can mess up pace/distance too.

Enabling 3D should never make that much difference. In fact, ion most cases difference between 2D distance and 3D distance is less than 1%. 

Here is an example. Let's say we are running a Vertical KM race and gain 1 km vertically within 5 km horizontal. That is pretty steep. The 3D distance will be sqrt(5^2 + 1^2) = 5.099 km which is below 2% difference with the 2 D distance and would never account for so much difference in the pace.

Agreed, but in conjunction with some of the other factors I listed, all those little differences can add up.