Steps to repro: 1. Create a new project with multiple connections (full1, full2, int1, qa, prod) 2. Set the default connection to int1 in the module. 3. Right click on module and select Retrieve MetaData 4. The MD will pull from Full1 by default, not by the module default (which, in my case is int1).
This could cause users to pull incorrect metadata if they aren't paying attention.