Sections of layers shifted on print surface

[JLAU]

I have a model I've created half a dozen times in 3 different 3D modelling softwares. I've sliced/printed both the original models and versions run through Netfabb Cloud. I've had others in the industry look at the model and they feel it is "clean". The majority of the print turns out great, but there are a few isolated sections in which portions of the surface are indented or raised. It's definitely not a mechanical issue as the surface on the other side of the "tube" print very nicely. I've printed dozens of other models and I don't get this issue. I have been battling this for months and I can't get it figured out. Tonight I am going to print the same model using Craftware and see how it goes. I realize there are other issues in the pictures of the prints I am posting as I was messing around with retraction settings. This is an ugly print, but the it is the one that makes it easiest to see the sections of layers that are "sunken in". Could these indeed be caused by retraction or related issues? I feel they are, but can't seem to get rid of them. I've included my .fff file as well. Any help/advice would be immensely appreciated. Thanks!

Jerome

[CompoundCarl]

Just to clarify, can you circle the area in that picture that you're talking about. It wasn't clear to me..

[JLAU]

Thanks for your interest in helping me out with this. I have circled the areas in question. It seems like they correspond to areas adjacent to the start/stop locations which makes me wonder if its something to do with retraction. The odd thing is I don't see this on other portions of the print. Its limited to the areas which have the holes. The best example of it is the lowest area on the picture that I have circled. You can see how that section is every so slightly offset from the rest of the surface.

[CompoundCarl]

I honestly can hardly see what you're talking about, so at that level, it's going to be really hard to pin point the problem. There's a lot of things that could easily cause that amount of variation. Machine vibrations, extruder dynamics, retract settings, the list goes on and on