I know this is a one-year-old post, and am sure by know you’ve found a solution or have tired and gone on elsewhere. For what it’s worth (and for any others out there that come across similar issues), today I had the exact same problem and couldn’t understand why, as I’ve been using DUIK for years without any issues. After some tinkering I found out that, for some odd, twilight-zoney reason, when I was pressing enter to change the name of my puppet points, instead of just highlighting the name and giving me the option to write over it or add something to it, it was straight off erasing the name, which I found strange but, anyway, thought I was going mad and this was actually the norm! But apparently that’s not the only thing that was happening, as you can see from the following screenshot:

Notice how the bottom names (“Snout”, “Neck Front”, etc.) all have a space before them as compared to the top names (“ear_tip_left”, etc.). The bottom names are the original names I placed, which produced the error. The top names are the new names I’m placing after realising there’s a space before the other names. The top names don’t give out any errors. (And, no, the error has nothing to do with using spaces as a pose to underscores.)
So for some weird reason, AE is now erasing the names and placing a white space when I hit enter to rename a layer. If I right-click and choose “rename”, it does what it’s supposed to do: it highlights the name and does nothing else.
The issue with DUIK in this case is clearly the white space before the name. But how that white space is getting there and why my AE is now just erasing the name and adding that white space when I hit Enter, I don’t know. I’ve tried the preferences to see if I’ve clicked something weird that’s activated this function but there’s nothing there that seems to control what happens when one presses Enter to rename a layer. It’s a twilight-zoney mystery!