Mpg4 editing problems in Premiere Pro CS5

I've been working with pp CS 5 or CS5.5 for a little while, and have hit a snag.
1.  I have a file that is an mpg file, created a long time ago, and has bad color balance.  over an hour
2. I imported it into After Effects, tweaked the colors, and exported it as an mp4 file.
3. It plays just fine.
4. I created a new project in PP, created a new sequence, imported the mp4 and put it into the time line.  It plays fine.  I need to clip spots out.
5. I set an in point and an outpoint on the main screen, and can see the bar with the timing ticks show gray between the inpoint and outpoing.
The timing marks are on the timeline, but don't extend down across the video and audio tracks.  I locked and synced the tracks.
Chosing ripple cut, I can move the inpoint to the outpoint, but it still plays the 15 frames between the in and out point.  I have used the extract icon on the main preview screen where I set the in and out, and still it doesn't delte anything.  I was playing around with some other section trying
to delete them from the sequence, and it says that all frames are in use.
I know this is pilot error somewhere.  It isn't working like the web tutorials show.  Is this because this is a compressed MP4 rather than an MPEG?  There is only 1 clip (the entire file) in the project.
The goal is to simply delete some bad sections where the talent hems, haws, makes a mistake and corrects himself etc.  I want to delete them and close the gap.  Any help as to what I missed would be appreciated.
Cheers
Woody

I know this is pilot error somewhere.
I would recommend reading the PDF file.  Go through from start to finish, in sequence.  Try each new thing as you learn about it.  Look up any words you don't understand as you go.
Once you have the data on how to use the program, chances are you will know exactly where things went wrong.

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