I'm trying to discover why some of my function responses are taking 2+ seconds every so often and I've noticed that on these requests the app insights End-to-end transaction details there are large gaps between each dependency call, which is where I'm losing all my time.
Can anyone tell me why these gaps exist and why app insights doesn't show what's happening during that time?
It's possible that your function has a dependency that App Insights doesn't automatically collect information on.
Please take a look at the list of current auto-collected dependencies. If your dependency is not there, then you will need to manually track the dependency.