It appears that the Pull from Salesforce operation is seeing that all the customMetadata records are updated on every request when nothing has changed. This isn't a huge deal but it's not right so I figured I'd report it.
Posted 14 May 2018
Thank you for bringing this to our attention.
We will consider our approach to pulling customMetadata and we will look for a way to improve it so that to avoid updating all the files each time.
I will keep you updated on the progress for this.
The Welkin Suite