Hi Markus,

This sounds like a very frustrating experience. See my comments in-line.

On Mon, Nov 11, 2013 at 2:59 PM, Mark Mandelkern <k...@zianet.com> wrote:
>
> LyX label and reference problem - faulty pdf
>
> This is about internal labels and references, as for theorem
> numbers and section numbers, not about the references at
> the end of a paper.
>
> These numbers should appear in an exported pdf, but
> at times the pdf will have only   ??   instead of the
> numbers, at more than a hundred places. The labels
> appear, but not the references. Thus, the exported
> pdf is useless.

Can you send (to the list) a minimal working example?
http://wiki.lyx.org/LyX/NewInLyX21

> Program restart does not help. Computer restart does
> not help. The only solution I have found is a complete
> reinstall of the program, including MikTek. And even
> then, it is necessary to go back to a previous saved
> draft, and re-enter many updates. Sometimes
> a day's work. Sometimes a crucial line is lost.

Doesn't this suggest that the problem is with MikTeX? Why do you think
it is a LyX issue? I really have no idea and it could still be a LyX
issue (maybe LyX triggers something when a new MikTeX installation is
found), but I'm curious on your thoughts.

Best,

Scott

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