I've not experienced this. Arch Linux has a good guide on setting up mbsync. However, the best documentation is really mbsync's manual... Although tedious, really understanding it makes things a lot easier and I believe would resolve your issues.
That's a reasonable hypothesis. My experience was mbsync would hang for many minutes, and eventually when I revisited the terminal it was in it had failed with a nondescript error.
I found, though, that mbsync failed to download updates after the initial bulk load.
Has anyone else run into this, and/or found a good way to use notmuch with gmail?