Trouble with MKV to MP4 Video conversions for Ipod

[Shisehise]

I have had lots of trouble with this conversion and could not find any information to help!
Here are some details about the problem:
The MKV files are very high quality (720p x264) with fine video and audio.
However, when I try to convert them into mp4 format and import them into itunes, the problem I have is that the frame rate of the videos are sometimes VERY choppy or that the audio sounds very deep and much like in slow motion.
I am converting the video codec to h264 or mpeg4 and the audio codec to mpeg4acc.
I am using Allok Video to MP4 Converter.

Any help on this topic would be appreciated! Thanks!!

EDIT: I am now trying mkvtomp4...

[hech54]

Handbrake and WinFF work flawlessly for me every time....however I know nothing about MKV files.

[Shisehise]

There was only one problem with the converter... the video and audio seems fine but now the file is not compatible with the ipod...
it could simply be the dimensions of the conversion... I will try it and get back to you guys

[teodz1984]

Could be the Dimensions (too big), COuld be the BITRATE (too high), could be the AVC PROFILE LEVEL (too high)....

When in doubt.. check here for the specs of your specific device... Please pay attention to what VIDEO and AUDIO specs it can play.
Use it as a basis for the settings of your conversion program. There are so many I-POD generations and variants around...

e.g. My 6th Gen IPOD CLassic's specs are as follows:

Video:
Apple reports that the iPod classic (6G) models support "H.264 video, up to 1.5 Mbps, 640 by 480 pixels, 30 frames per second, Low-Complexity version of the H.264 Baseline Profile with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; H.264 video, up to 2.5 Mbps, 640 by 480 pixels, 30 frames per second, Baseline Profile up to Level 3.0 with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; MPEG-4 video, up to 2.5 Mbps, 640 by 480 pixels, 30 frames per second, Simple Profile with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats."

Audio:
Apple reports that the iPod classic (6G) models support "AAC (16 to 320 Kbps), Protected AAC (from iTunes Store), MP3 (16 to 320 Kbps), MP3 VBR, Audible (formats 2, 3, and 4), Apple Lossless, WAV, and AIFF."