It's highly unlikely that it's Cisco related. I'm sure your provider doesn't know better and hard codes all the interfaces 100/full. It's a common misconception that it's good to do that, in reality no networking vendor including Cisco recommends doing this. I'm sure if their side was set to auto it would work fine. 100/full connecting to auto == duplex mismatch.
With the media and mediaopt in your config, you're set. It won't ever get overwritten or anything, it's a fully supported option, it's just that since so many people don't understand autonegotiation we hide it to prevent people creating performance problems by forcing when they should leave everything to auto in virtually every circumstance.