Ok, I complained about this quite a bit and was passed up to Level 3 Support (System Admin) at my host. This is what he said:

Can I have your admin login details for your youtube site so that I will test it in my end, we have the Max_execution time set to 1000 in our master php.ini and in your local .htaccess settings its set to 9999, so it should handle that size of files very easily.
So now all of a sudden it is up to 1000. This is probably true. I just uploaded a video that took 12 minutes according to the upload progress bar, and it was successfully completed. Now, will it stay at 1,000? Only time will tell. lol