Tick "Set custom group ID" too.

If you have the correct options ticked, SimPE does "Fix Integrity" while you're cloning (the box where you give a new internal name to the resources), so you don't have to do it again manually**. Reasonably sure it's the "Set custom group ID" that adds this.

I've noticed the CRES issue sometimes happens after "Fix Integrity" if you have a resource selected, or start working on the item immediately (changing the mesh, etc., especially while resources are still unsaved/showing in italics). If I have to do "Fix Integrity" (rarely for objects since I've found a few ways around, and always for CAS meshes), I save progress first, reopen the file (and make sure no resources are selected/showing in the Plugin View - reopening the file seems to be the only thing that clears the Plugin View), do "Fix integrity", save the progress, reopen the file, and start working. This has cut down the instances of this happening from somewhat infrequent to about zero.
(I do "File-> new" or click on the "new file" icon that looks like an empty paper, and drag&drop the file in, so it's not a tedious step to reopen the files)

I have been able to trigger the issue knowingly, if not every time, by not following those steps.

I don't know what spesifically causes the issue, and I don't know if there's a fix for it other than starting over the file, so I just go for my tried and trusted "better safe than sorry" option above.


** There are reasons for doing "Fix Integrity" again, but in some cases it can be handled in other ways. Adding subsets for instance - you can use the "Fix TGI" button in the Plugin View to make the clone separate for the TXTR and TXMT, and in the MMAT you can set the clone to one instance number up (usually from 0x00005000 to 0x00005001).
Personally, I was just tired of the occasional borked files...