Thank you for contacting us with this question.
Salesforce has a very tricky mechanism for working with profiles - the content of a profile file depends on what other items were pulled at the same time from your organization. Additionally, this approach does not allow the IDE to check if anything related to the profile was changed on the org side.
As operations with profile files are "not-so-common" we are not pulling the whole org together with profiles (because this will completely slow down the normal working process).
Due to this reasons, it's possible that after pulling your profiles from the organization, these files would have another information comparing to what you'd get if you pull entire org using Ant or any other tools.
In case if you are not doing any changes in the profiles in the IDE but still need to maintain them in the Git repository with the full data we suggest you excluding profiles from The Welkin Suite's project and manually pull them using Ant task before commiting/pushing to the git repository.
If you would have any other questions, please contact us. We will be happy to assist.