Thank you for your update.
According to the log file which you sent to us, the reason for the issue is the same as previously. This means that your Ant tasks are not related to the issue, and this is caused by files on your Salesforce Organization.
I kindly ask you to open your Org on Salesforce and please check which files have the same names and are located in one folder. You can check this for Dashboards, Reports, and Email Templates. However, I want to draw your attention that the files with a duplicated name belong to the same metadata type.
TWS detects these files on the first stage of pulling when Salesforce returns the list of available files. The pull process itself doesn't start because of this.
Exactly this information will help us to understand how we can solve the issue and, as a result, we will be able to tell you when we could do this.
The issue appears on the Nova R2 version of The Welkin Suite because we implemented the support for dashboards, Reports, and Email Templates in this version.
We will appreciate your help greatly.