I tried uploading a BAM both from a desktop and with a URL, and both worked at UseGalaxy.org. All went fine, same as the test from Igor with the GFF3 data.
More help for Upload → Getting Data into Galaxy
So, everything seems to be working at the ORG server. If there is a problem at a different server, or with a different file type, you are welcome to share back more details. How to share work is in the banner of this forum. Thanks! 