Thank you for your bug report.
May I please clarify with you if the 'Subscribe' option is enabled for your Static Resources metadata type in the Project Metadata Components? This functionality detects the new files on your org and downloads them automatically during the pull process.
To verify this, please open the context menu for your project in the Solution Explorer and select the 'Project metadata components'. If the 'Subscribe' option is not highlighted with blue, please click on it.
If there are new files on your organization, they will be present in the Pull wizard in the appropriate list.
The first list which appears during you pull is the list of the files which will be verified for any changes. These files are already present in your project.
The second one will appear if the IDE detects new files for the required metadata types.
Our team will investigate this issue and your answer will help us to reproduce it or understand the reason for it.