The problem is almost certainly your conversions.
it is not my conversions. The files all play perfectly in itunes on my mac mini and as a test I moved my Apple TV to my basement and I used a wired connection instead of wifi and it is working now; all files. I believe that the new software updated did something to the wifi and this is the issue. I never had any problems before the update and I get excellent wifi signal where I had my Apple TV before. All my problems have been since the stupid update.