A long time ago I used a much older version of Premiere to edit my videos. It didn't have as many fancy features, but it worked. Now, I'm concerned. I'm using 5.5.2 and it's actively corrupting my video files as I edit them. A clip that I will scroll through that is smooth in the source material will become choppy the more I view it, skipping frames and repeating frames as if it's stuttering. Places where I put clip beginnings and ends will shift a few frames with no modification on my part. Worse yet, these errors seem to propagate back to the source material in the project.
The original files I had were MKV, but since Adobe doesn't support them I used a conversion tool to convert them to WMV. Was this a mistake? Is this a common problem with 5.5.2? Does anyone have any advice as to how to fix this before it eats all the progress I've made so far?