Multiple part / Multiple extension Issues

Hi All - I am retrying this thread here hoping that someone has had and solved this issue. There were a couple of other issues that were in my other thread that I have omitted from this thread as they have been solved.

Issue: When printing multiple parts or parts that have multiple extension that some off of them I get errors where the printer will not put the first layers after a move in the correct location (see pics). This does not happen when printing a single part. It also does not happen when printing a large part. I.e. I can print a dome and it comes out great. It can even cross the center and not have an issues. However, if a layer has two separate perimeters then it has the issue.

If a part has 3 perimeter layers, only the outermost layer is wrong. The others are correct. Also, the parts that have this issue are quite weak. They break apart easily.

I have tried:
Retraction settings - I'm not getting and strings between parts or extensions
Checked bed level
Checked belt tension
Checked extruder settings. Correct extrusion length and speeds
Speed settings - I have tried it on fast and really slow settings
Scale - This happens to large and small parts of different scales. The issue scales up and down with the part
Upgraded from Slic3r 1.0.0R2 to R3

Setup:
Custom Delta-pi
Latest marlin firmware
Slic3r 1.0.0R3 run from Repieter-Host
Sometimes I print from SD, Sometimes I print from Repieter-host

I'm wondering if it might be in the file itself. Slic3r can fix files within itself but some results are unpredictable.

Is this a .stl you designed yourself or did you find it somewhere? Can you share it?

Have you printed multiple parts of something else with the same problem?

I'll post the file tomorrow, its on my office computer. Its a file I made, but it happens with any file that has multiple extensions or multiple parts. When printing through repieter-host it shows the current layer path of the printer and it even shows everything correctly. Not how it is actually printing.