> [a href="javascript:ShowMenu('123/$FILES/My file
> here_12.docx','window')"]test[/a]
> Then the link inside the <a> tag is nout found!
> 
> [a href="javascript:ShowMenu('123/$FILES/My file
> here_12.pdf','window')">test2[/a]
> it works.

> Please fix this.
Problem must be on your end, not httrack.
Try setting a mime type docx <=> application/msword
If that works, your web server needs adjustment.
Alternatively, you can enable and look at the hts-ioinfo.txt at what the
server returns.