I just tested it to be sure and yes, it's working correctly too.
I created two DB instances, on 3306 and 3308. I created DB db3306 on port 3306, and db3308 on port 3308. Here are the results:
When I proceed the import, Skipper correctly shows table3308 imported:
So I'm sure the import process is working as expected. The issue you're describing has to be caused by something else in your configuration.
If possible, please simulate the same process with dockers as I described here.