Do not know if those who develop SP follow these forums, but this post should be considered a bug report
Users indicated they were unable to set for a few items the multiple choices in a doc lib choice column with multiple selections enable. Other items did not have this problem.
A search for others encountering this issue appeared to indicate that the documents of these items had "custom XML" in them that was interfering with this setting. I did not make the connection with our situation, but another helpdesk person said he experimented for a while and found that it was the Office doc (Word, Excel, etc) Document Properties internal metadata feature that was preventing SP from setting the multiple values in the doc lib column. It was after clearing the Document Properties and Personal Info (File->Info->Check for Issues->select Document Properties & Personal Info->Remove All) that the SP column accepted multiple selections.
This is a workaround clearly.
I understand that SP list/lib metadata is integrated with value settings of Document Properties with Office documents, but this is unexpected (i.e., buggy) behavior shown to the user. A fix should be requested.