I use MikTeX under Windows with Ghostscript/ImageMagick/etc. I also found put the class paper.cls and it's layout in d:\programme\texmf\tex\latex\base as I did in Linux. Ater taht I turned to MikTeX Options and refreshed the file database AND I reconfiguered Lyx.
the layout should go I think in \lyx\share\lyx\layouts (or ~\.lyx\layouts) followed by LyX reconfigure, otherwise it doesn't know where to pick it up.
Milos
