Saving movie with QT7Pro as good as frame-by-frame conversion?

I use Aimersoft's Video Converter Ultimate to convert videos into .MOV files, from say .flv, .AVI... but I know that I can simply open the video in QuickTime Pro 7 and save it as a MOV in a fraction of the time. I'm pretty sure the conversion software I use from Amiersoft converts each frame, while QT7 will just encapsulate the video, but am I right?
I'm worried about compatibility issues down the road and whether the saving option is just not as good. I'm not a pro and only do it so I have everything in MOV format (which I find easier to manage in the OS X environment), it also allows me to save metadata into the file. Will there be any issues, like quality?
Thanks!

You want to "convert" (Export) rather than "Save As" when the codecs used in the file are not natively supported by QuickTime Player.
Flash video and some AVI's use the Perian component to play via QuickTime. Putting these codecs in  QuickTime .mov container (Save As) may not work on other machines.

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