Fade in & Fade out Clip trouble

Hey guys, so I'm fairly new to Premiere and I still have a lot to learn. Apologies in advance for potential obvious questions.
In Premiere Pro CS5, I'm currently having an issue where the fade out/fade in transition between two clips results in a sort of skippy/choppy section of clip.
The original clips are fine when they are by themselves, but when fading out/fading in over each other, the problem occurs
I've attached a youtube link to the link to clarify.
Here's some info about the clip if it may help:
-The original clip was recorded on Garry's Mod (Game), using the built in Source Recorder. The original clip was a .dem file
-The .dem file was converted to a .webm file using an in-game converter
-I used VLC Media Player to convert the the video from a .webm file to a .mp4
On another note, how do I get the exported video resolution to match the sequence resolution?

Hi,
Check this example.
http://adobe-center.net/devnet/flex/quickstarts/defining_state_transitions.html
It uses Resize effect with some filters. You can use the same technique to get the Fade effect

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