Editing Help for Video Software Rookie

[proteusmp3]

Hi,
I'm trying video editing for the first time with Avidemux.  I've read through the wiki and didn't see an answer to this question.
I didn't have any problems with Avidemux at first, and was able to cut out scenes from several mp4s.  Then, I began getting a warning message before saving, telling me that my edits might impact image quality.  Now, I've had several videos turn into a murky orange mess for 5-10 seconds after every cut scene.  What can I do to solve this?  I've been leaving the two encoding options as "Copy" because I know very little about encoding.  Finally, I did try choosing two mp4 options for encoding, but the program only saved 1/3 of the total video.
So, my question is...what should I change the two "Copy"s to?  I'm editing mp4s ripped from a DVD-R.  I'm using Windows 6.0 (Build 6002 Service Pack 2).  My Avidemux is version 2.6 (32-bit). 

Thanks for any help.

[Jan Gruuthuse]

ripped from dvd. If that did change the video codec and audio codec it is hard to tell what is going on.
Use the original .vob from your hard disc. When avidemux asks:

There are several files with sequential file names. Should they be all loaded ?

reply: no. Append additional files manually with [Ctrl][A] (press simultaneous).
Select cut point(s) only with keyboard up/down arrow and mark [A ] or [ B].
In main menu: Edit: Preferences: [Video]: Default Postprocessing unmark
[ ] Horizontal deblocking
[ ] Vertical deblocking

[styrol]

Now, I've had several videos turn into a murky orange mess for 5-10 seconds after every cut scene.

As Jan said, only cut at keyframes otherwise information is lost due to deleted keyframe needed for decoding. In your movie there seems to be a keyframe every 10 seconds.