Bit of a mystery.
What I recommend:
Select 1 track
Choose Tag, this opens the tag panel and click on the file name at the top.
This gives you a list of the tags as they are inside the file so “hard coded”.
Don’t know what file format you are sending to the iPad, probably not FLAC?
Anyway, check if there is a tag TRACKNUMBER (FLAC) or TRCK (MP3), etc.
Screenshots can be found here
http://thewelltemperedcomputer.com/SW/Players/MC14/MC14_Edit.htmIt here is such tag (likewise CDNUMBER) at least it is clear that JRiver populates them properly.
If this is the case, you might do the reverse.
On the iPad, fill in tracknumber, cdnumber, etc en transfer back to JRiver.
Maybe the iPad (the media player you use there ) uses other tags.
With the same trick as mentioned above, you can inspect what has been written hard coded.
Success