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It's tough to understand what's happening from text only, but a couple of things come to mind.
I'm assuming that when you said "cut-out" you are meaning the "cut out" feature in assy where you use one part as a "tool" to remove material from another. If this isn't the case the first of my ideas won't apply.
First, I'd make sure the accuracy of both parts are identical. Use absolute accuracy and set them both the same.
Second, look for any geometry checks in either part and try to resolve them. Geometry checks can lead to odd behavior like you're seeing.
To start of, this is not top down design, where I start in an assy and make parts as I go. This is a straight up part made in its own. As in an assembly, if you select extrude the only option you have is to remove material. But while in a part file, extrude feature will add or remove depending on if I select the remove option.
Furthermore, it seems this problem does not even pertain to the specific part I originally inquired about. I created a new part making a 10 inch circle extruded out to 2 inches, then I made an 8 inch hole centered inside this circle. How this hole is created does not matter. I tried 3 methods, first I made one solid extrude of the 10 inch circle, then created a new 8 inch extrude with the remove option selected to create the hole. my second method, I created one extrude with two circles in the sketch, one 10 inches and the other 8 inches. My third method, I created one extrude of a 10 inch circle, then I created an 8 inch hole with the hole feature, again centered inside the 10 inch hole. All three of these methods gave me the same result with my slot that follows the outside profile of the 8 inch hole.
This problem seems to be specific to my dimension (also yes, I always use locked dimensions. I never leave a dimension available to be dragged out of sketch). When I create this slot that follows around the outside, it does not matter how deep the slot goes, I tried a shallow slot of only 0.050" deep to a full depth of 2" deep. This is the kicker, what seems to make the difference is the distance this slot is away from the inside hole. More specifically, if I have the distance as .1" offset, the hole is shown the next time I restart the program and open the part. But once I move the offset of the slot .099" restart the program and open the part voila, the graphics is messed up again and there is a surface showing where the hole should be.
I've uploaded some pictures of the part. I hope they are showing in the order I created and named them. The first (extrude1) should be the extrude in shading display style with the hole not visible. This is my issue, as anytime I have the part that has this slot around the outside edge this happens.
My second and third image (extrude2 & extrude 3) show why this is a graphics issue and not a physical part issue. The second image shows when I hover my mouse over the surface it shows the inside wall of the 8 inch diameter and does not highlight the surface that should not be there. The third image is in "no hidden" where you can see it shows as it should, although once I switch back to "shading with edges" this unwanted surface appears again.
My fourth image (extrude 4) is just to show my sketch of this part, this image is from my second method as mentioned above, where I just had two sketched circles and the following extrude makes a "tube".
My fifth image (extrude 5) shows the slot that is created. In this image I have the dimension set to 0.099" and from this dimension and lessor, this problem seems to be consistent. Again, once this dimension is 0.10", this graphical error does not seem to occur.
My sixth image (extrude 6) shows what the part should ultimately look like (in this scenario), you can slightly see the white background in the slot as this is where the slot follows all the way through.
hope this helps understanding my problem.
Edit: I've added three more pictures. They are of the modelcheck option from the File>Prepare>modelCHECK Regeneration. Here I get lost and have no clue as what this pertains to but thought maybe this could be similar to geometry check. The result of this modelCHECK does not change when I increase the slot offset above 0.10" though and gives me the same result.
I am unable to reproduce the issue using Creo 4.0 M060 or Creo 220.127.116.11. Would you we willing to upload your test model?
What is the trick to uploading the part. It does not allow my part to upload as it states it has an invalid extension, I'm assuming due to having .prt.11. Do I simply remove the .11 and the file will still be readable for you? Also I am using Creo 4.0 F000. Maybe I need to install the updated version.
I tried to go ahead and remove the .11 extension on the .prt file, but I am still getting a message that this is an invalid file extension. If I remove the .prt as well from the file name, I get a new message showing all the allowed file types, what is odd is .prt is in that list, so I am confused to why it would not allow it to upload after I removed the .11 extension.
Edit: it claims, the contents of this attachment does not match the file type.
"Cutout" is a Creo function in assy mode which why I thought that's what you were doing.
This does seem like a graphics issue. What graphics card are you using?
Try setting the config option "graphics win32_gdi". This tells Creo not to use your graphics card so if the issue goes away, it's your card or driver. You don't want to leave this option set, it's a diagnostic tool only. It looks like you'll have to add it manually via a text editor as it no longer shows up in the options list, although I believe that it is still valid.
I'd still look at your accuracy (File > Prepare > Model Properties > Accuracy). Use absolute accuracy and set it at 0.0001.
ModelCheck is not the same as geometry checks, although I believe that it will report them if found. Geometry Checks can be found on the Tools tab in the Investigate section. I none are present, it will be grayed out.
My graphics card is a Nvidia GeForce GTX 1050, I use a consumer level laptop and it is not a workstation. My driver did happen to be outdated but updating it did not do the trick. .
My accuracy in model properties was at 0.0012 and I updated it to 0.0001, but I can't make it absolute as you said to do, it only says relative and gives no option to change that. So I located the option to set a default absolute accuracy in the config editor and after saving and restarting the program, the problem still persists
I added the graphics option to the config file, and confirmed it added when checking in the editor in the program, sadly this did not change anything still.