Any recommended way to convert mkv to mp4 for iPad usage?

[Undead]

Do you guys recommend any ways of converting mkv files to mp4 files?

I only know how do to this with Handbrake, but the audio ends up sounding washed out and irritating. Alternatively, any recommended settings for improving Handbrake's conversion of audio would be appreciated.

It wouldn't be sensible to ask this if I wasn't using an Apple product... (It's a device given to me by my school until I exit ninth grade, don't blame me)

[Dancso]

If you're using their ipad preset, make sure it doesn't fiddle with the audio channel settings. (Though the version I have suggests 160kbps with dolby pro logic 2 for the ipad, which should be ok)
Also, I'm really not sure about the exact specs of the ipad, but you could try to change it to another mixdown, perhaps even mono, see if it sounds any different, on an ipad it might not matter. I've converted videos to mono in the past to save space on my teeny tiny phone, and the sound felt okay to me.

[Undead]

I found that changing the audio codec from AAC (avcodec) to AAC (FDK) improves audio by a large amount. So I consider the case closed now.

[irukanjji]

Check this out:

Free Video Converter
http://www.freemake.com/free_video_converter/