I don’t know what is the reason for this behavior, but there are a few things you can try to do to get more info:
I notice the thread that calls vkQueuePresent appears to block during the call (as is usual) but during the long calls it then performs CPU-intensive work for ~7 milliseconds. You can take a look at the CPU sampling points that were collected during this duration and to see which module is performing this CPU work. Most probably it would be the graphics driver.
Enable GPU Metrics collection and capture another trace session. Look for memory transfer activity during the extended present calls - the app may be performing a lot of buffer migration.