I forgot about encoding params and how iTunes needs this to report the details of a file. Sorry for that! I'll try to preserve the data with both Reuse unmodified MP4 atoms enabled and disabled for the next version.
This was the default behaviour for ID3v2-based file types. MP4 tags tried to reuse unsupported atoms for quite some time and it was only streamlined with the newly introduced settings to behave consistently with ID3v2 tags. Looks like there is no ideal solution for this (cf. also, the Xtra ratings from Windows Explorer, which we discussed recently).
And it turns out that you've observed the same behaviour reported here already a few weeks ago: