Thank you for bringing this issue to our attention.
The reason for this is the next:
This is related to changing a process builder's name when you change its status to active: when you create a process builder file on your Salesforce Organization, it is inactive and its name contains the suffix with the version, and when you make this process builder active - the suffix is removed.
The IDE doesn't handle this correctly and this is why you can download to your TWS project process builder files which have the default name only. in other words - only inactive ones. Our developers will work to solve this issue.
I will let you know when you will be able to pull your active process builders.
If you have any other questions, please share them with us. We will be happy to assist.