Well this is not a bug. :-) The first problem has to do with the way as lyx2lyx does not yet reads layout files.
In this case instead of issuing \begin_layout Standard it issues \begin_layout Since the unknown layout are converted to the default layout this works. There are some problems here. The first is to assume that Standard is translated to latex with no markup as in latex we can signal a paragraph just by inserting an empty line (there are other ways but this is the most used). I will try to illustrate the problem here, the following latex is translated to lyx as: ---- latex --- \vspace{2cm} Simple par \vspace{1cm} --- lyx \begin_layout Standard \begin_inset VSpace 2cm \end_inset \end_layout \begin_layout Standard Simple paragraph. \end_layout \begin_layout Standard \begin_inset VSpace 1cm \end_inset \end_layout ---end--- One (easy) option is to change all the empty layouts to "Plain Layout" like what we do for table cells. This would remove the first warnings. Any objection? -- José Abílio