Windows tend to be tricky when modifying files through an open dialog window. Out of curiosity, which version of windows are you using? I'm on win7 x64 SP1. Those simple changes should indeed not cause any quality loss. For Fraunhofer AAC, I found a blog post with the process that seem well enough explained to compile it for windows so I'll try to compile it this weekend so I can give it a try. The link: http://taer-naguur.blogspot.ca/2013...with-fdk-aac-lib-on-64bit-windows-how-to.html For the processing done by MeguIVit, there's nothing more that would benefit from an upgrade I believe unless QTGMC itself had a newer version. To compare videos, I use a small software a guy made on doom9 where you load 2 video and you can click on the picture to switch between one and the other. I don't use it that often though since it's too old to support 10bit videos and those are what I encode the most in. If you want it, here's the thread: http://forum.doom9.org/showthread.php?t=138430 There's also the SSIM metric for video quality, but it's not super reliable since it's data calculated by a machine and doesn't match our perception of picture quality perfectly. The thread about it on doom9: http://forum.doom9.org/showthread.php?p=370060#post370060 Most of the time, I just make multiple samples with different settings, play them back one after the other and trust my eyes to tell me which is generally better or if I can't notice a difference. It's always best to compare video while it's playing since a single frame could look better when stopped and it could look horrible during playback if there's some moving artifacts or things like that. Edit: For your problem with fhgaacenc not taking AC3 as input, you can use a software to convert it to wav(or some other uncompressed format it can use) and pipe it to it. For nero, I use avs2pipemod(since I use an avisynth script as the input) in command line and pipe it like this: Code: "avs2pipemod.exe" -wav "input.avs" | "neroaacenc.exe" -ignorelength -q 0.42 -if - -of "output.m4a" The | means the result from the command on its left will be used for the command on its right. A - is used for the input on the command on the right(after the -if in this case).