Playing AC3 in iTunes

Hello, I have been playing movies with AC3 audio for many years now in QuickTime (with no problems) and have now been interested in organizing them within iTunes. I've been converting all movies in "HandBrake" and basic settings are as follows.

Format: .M4V

Video Codec: H.264

Audio: AC3 5.1 Channels

Output Size roughly 4GB each

To import them into iTunes I have been using iFlicks. When the process is complete I play the movie and it works but there is no audio, however when importing a TV show (The Simpsons) from an unknown source into iFlicks with settings shown below it plays perfectly fine.

Format: .MKV

Video Codec: H.264

Audio: AC3 5.1 Channels

File Size roughly 400Mbs each

I don't understand why one clip can play perfectly fine with AC3 and the other cannot. Has anyone come across this problem before or know a fix?

Thanks