I have a video clip which is about 1 minute long.

In the middle of the video I want to cut out a section which is 5 seconds long, slow down that part and then repeat it several times.

The problem is that when I cut out the 5 second section and then try to slow it down or stretch it out or move it around on the timeline, it acts and if it's still just a part of the main clip....so it put back in frames from the main clip etc...

Is there anyway to "permanently" cut a section of a clip, so that the cut section is now a new clip that can be modified and has no other frames in it?

Once you cut a clip (with SHIFT-R) the cut sections can be manipulated independently of the rest. What you described should be doable w/o any problems. You need two cuts, obviously, to create 3 clips with the second one being the one you want to slow down/stretch.
Please note that when slowing the cut clip down, aka stretching it, you need to make room for it otherwise kdenlive wouldn't be able to do it. I am assuming you moved the cut clip to a different video track (also keep in mind that you need to have a corresponding audio track available if there is sound) so you should be able to stretch it and then move the right portion of the original clip to the right far enough to have room in between for the cut and stretched clip.

davidisaskingquestions wrote: it acts and if it's still just a part of the main clip....so it put back in frames from the main clip etc...

What version of kdenlive are you using?