Why is Compressor so Slow?

I love Apple software, and Compressor is no exception.  For converting and compressing video, there isn't a tool out there that surpasses it.  However, there is one major complaint that I have.  While the rendering process of the video itself is relatively quick, the process of setting up an encode is grueling.
The other day, I took a video file (it was .mkv) and imported it into Compressor with the intention of formatting it properly for my Apple TV.  However, importing the video file itself took almost 3 hours.  I thought the program had frozen, but I left it going just to see if it would recover.  The next step was to take a preset and drag it into the project file for the conversion.  This took another hour.  Hitting the "Submit" button to start the conversion took 30 minutes.
The conversion process itself was relatively quick, and finished in under 2 hours (not bad for a 3 hour 1080p movie).
I love how this software works, and I love how easy it is to use.  But the process of starting a conversion or compression should NOT take most of a day.  I understand if the rendering process itself takes hours, but it seems silly that setting up a project takes that long.
Is this a bug, or is this normal?
Or perhaps it is simply the .mkv file format there is a problem with?  When I am sending footage directly from Final Cut Pro X, there seems to be almost no delay, even when the video project I am working on is over two hours (also 1080p).  Either way, I am using the freeware "Handbrake" for my Apple TV conversions, which seems silly since I have a perfectly functional Compressor program at my disposal.
Thank you for listening!
-David
P.S.  If it mattered, here are my system specs:
Early 2011 MacBook Pro
2.2 GHz Intel Core i7
8 GB DDR3 RAM
AMD Radeon HD 6750M 1024 MB Graphics

Not saying that Compressor is speedy, but for most audio and video formats, it's just drag and drop and Compressor will open them. But…MKV isn't one of those formats. I understand that he newest (beta) version of MPEG Streamclip supports MKV. You can export it to something that is Compressor-friendly.
Good luck.
Russ

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