We have had very similar sounding issues on occasion. I believe it's happening due to an improperly built package, but we have not definitively determined that.

In our case (possibly not yours), the Keychain related files in the default user template folder were missing/corrupted along with a few other items. If you go to ~/Library/ does Keychains show as a folder or does it show as a file with a size of zero bytes? If it's the latter, we were able to correct the issue for the logged in user by deleting the file and restarting. If someone else logs in to the computer in the future, they may run into the same issue.

Usually this is an error with using FUT/FEU from Composer (likely from bad permissions). It's a terrible way to do things, and one that really never should have been done.

There are a number of vendor supplied packages as well as poorly created composer packages that put zero k files in place of keychains, as @jacob.edwards said, just deleting these usually resolves it.
The other thing that can commonly cause keychain issues is the drive running completely out of space, although this is usually resolved as soon as space is made available. I have had failed JAMF policies that completely filled the drive do this a couple of times.

@ewettach were you able to find a solution to this issue?