My installation is lyx-qt 1.3.3win32 and miktex 2.4 on win98 (first edition)>
But: reconfigure does not work. There are no TEX-classes, style files... So I can't do any serious work.
Did you use the menu Help -> LaTeX-Configuration? This menu is broken in LyXWin and says nothing about the success of the reconfiguration.
Old lyxfiles are not recognized. "not a lyx file"
Yes this a big problem with LyXWin, but it is possible to convert the files manually with the file "lyx2lyx.bat" (if you browse the mailing list archive, you will find a detailed description).
Another way is to load and save the files with LyX 1.3.x on a Linux system.
But I made the experience that LyXWin runs very unstable on Win98 machines, better use Win2000 or WinXP. And if Win98 is really necessary, you should at least use the second edition ;-)