Partial footage/black screen when replacing footage in PPro CS5

Question

Let's see if I can get all the relevant info down here.
Started off with a project in PPro CS5; using two source files (one an MP4 from a Flip cam - not the footage I am having an issue with) the other a direct-stream feed from a 3D application, converted to Lagarith. Both were dragged into the timeline and manually synced so the footage matches up - the MP4 is overlayed over the direct-stream in the corner of the frame, scaled down.
I have been using the razor tool to cut both sequences into short clips at the same time in the timeline to maintain identical in/out points. The Lagarith-encoded stream is lower resolution than I would prefer, so due to some other additional factors I have taken the stream and scaled it up from the original 640x360 to 1280x720 using a neat app called "Video Enchancer".
Now, here comes the issue; I have been editing with the 360p footage, and would now like to replace it with the 720p footage (basically proxy editing). "Replace Footage" function to the rescue, right? Apparently wrong.
Once I replace the footage, most of the timeline gets diagonal stripes across the cut clips, as well as a black screen in the program monitor for preview - indicating that the footage is still missing (though no red "media offline" image). Oddly enough, of the three 360p original files I used to edit with, the first replaced perfectly fine, the second replaced fine up until a certain point, and the third didn't work at all.
The oddest thing of all, however, is that I can view the replaced footage in the source monitor without any issues, and PPro reports no issues with either the video or the audio stream (audio is uncompressed PCM WAV). I can even drag the replaced footage (now 720p) into the timeline, and watch it in the program monitor.
The scaled-up 720p footage is of the exact same length as the original 360p footage; down to the frame count. Both are using Lagarith - yet for some reason, replacing the 360p footage with my scaled 720p footage doesn't seem to work correctly. Even selecting "reveal in project" over one of the cut clips that shows no video/audio points me to the correct source file!
What's going on here?
If there is any additional info you would need or like, feel free to ask and I'll provide it. Sorry for the long post.

Answer 1

I'm editing my reply, and going to post a new thread, as I figured out at least what the issue is: PPro is not detecting the correct duration of my footage.
Message was edited by: XNtricity
Reason: New, more succinct question needs to be asked, as root cause of problem was discovered.