Problems with AAC AND AC3

Hello,
I just got my new AppleTV and sadly have some problems with my videos containing AAC Stereo and AC3. If I use handbrake my first audio stream is AAC and the second is AC3. These videos just work fine. But if I use mkvtools to change the container my first stream will be AC3 and the second stream is AAC. If I play these files on my AppleTV I just get stereo...
If I delete the AAC stream everything work fine, but I will probably have problems playing those files on an iPhone or iPad because of the missing AAC stream.
So is there any way to change the stream order? I've tried subler, but I can only delete or add streams, but not change.
Does anyone have an idea? how to get rid of the problem?

Thanks!

Thank you sooooo much

BlackMangoTree said:

What version od MKVtools you using

2.4 had an issue with AC3 audio was fixed yesterday. in version 2.4.1

Click to expand...

Good to know! Do I have to reconvert the videos I converted using 2.4? I've used 2.4 beta for a while and 2.4 for about 4 days. Do you know what exactely the issue was?