CopyProfile in Build 1607 not fully working?

I've encountered a strange behavior of the CopyProfile feature in Windows 10 Anniversary Update. We typically create our images in Audit Mode on a VM and use CopyProfile in the Answer File to make sure all users have the same visual experience. This includes not only the Start Tile layout, but also general settings like: always show all icons in Notification Area; File Explorer opens to This PC instead of Quick Access; and most Startup items being set to "Disabled" in the Task Manager's Startup pane.

Until recently this has always worked without any problems (since they fixed it with Build 1511 of course), but in the last two weeks every time I pull a new copy of my image the Start Tiles are fine, but NONE of those other options I mentioned get carried over into the new Default profile! I know the CopyProfile switch is being processed because the layout of our Start menu is as I expect it to be (no tiles at all, only the All Apps menu), but that appears to be the only aspect of the profile being carried over. I pride myself on the appearance of my image, and I'm admittedly fanatical about my notification area and especially File Explorer opening onto This PC.

Has anyone else had this same experience? I don't know of anywhere in the image offhand that I could have accidentally chosen this behavior...

Any advice would be greatly appreciated!

Between Friday night and early this morning we've rolled back our VM through several checkpoints and tried again. The CopyProfile switch seems to work as intended in Build 1607, as far as I can tell. There are several of us working on this iteration of our image, and I'll confirm with my staff if anyone tried to "clean" the Default user profile before I pulled the test copy Friday morning. In all likelihood the handful of settings that didn't get copied were probably kept in some kind of database file under the hidden AppData user folder, which we sometimes try to shrink down to decrease login times. Thank you for your offer of help, Kari!

I've confirmed it - one of our technicians did a "clean up" of the admin profile before we pulled the image that experienced these problems. It appears that one of the deleted folders caused these settings to be erased; subsequent testing confirmed the CopyProfile feature to be working normally.

In other news, we've started playing with the LTSB Windows 10 v1607, which comes with none of the system apps. Initial login times are back under one minute, but it we've run into trouble with Taskbar icons not coming through with CopyProfile. It doesn't matter at the moment, as we've worked around that by adding File Explorer to the Start Menu for now. We have technicians working on this new issue and searching other threads/forums for more info. Thanks for reading!