I would say that is the most likely cause. ID3 has numerous 'overlapping' fields depending on the version of ID3 being used (v1 and v2 are completely different in their implementation, and in fact neither of them is an actual 'standard'). The fact that the same files show consistently would indicate that it is not an issue with the head unit per sae, rather a compatibility issue.
Try editing a 'problem' file in the music player of your choice (mine is Winamp because I'm old skool, but you might to use just a tagger like mp3tag) and check its ID3 fields against a 'good' file to see if there is a correlation.
You then might want to batch process your MP3s to copy the ID3 v1 tags to ID3v2 or vice versa.
There may be a firmware update for the RCD available which may improve the compatibility with various tags. These aren't available on CDs like for the RNS, I would suggest talking to Transporter who can probably check if there is an update for it.
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