I've found what appears to be a bug. It's related to labels. If a document saved with LyX version 1.1.6fix4 has labels that include underscores "_", then the label name is changed when opened with LyX version 1.2.1, causing unresolved references.
Label Changed to
name_of_label name_{o}f_{l}abel
second_label second_{l}abel
Hope that helps.
Roberto
