I use MUI heavily with OS 3.9, there's no problems I know of.
For a start make sure you have something like this in your user-startup sequence:
if exists "Sys:MUI"
assign MUI: "Sys:MUI"
if exists MUI:Libs
assign add LIBS: MUI:Libs
endif
if exists MUI:Locale
assign add LOCALE: MUI:Locale
endif
version >nil: exec.library 39
if not warn
if exists MUI:Docs
if exists HELP:dummy ; do not remove
endif ; this entry!
assign add HELP: MUI:Docs
endif
endif
endif
Sorry if that looks a bit messed up, I think the line spacing will get striped when I post this.
Also it may be worth tidying/repairing/upgrading your current MUI setup with this archive:
ftp://mp3:mp3@amiga.serveftp.net/Uploads_here/FullMUIsetup.lhaBe sure to read and follow the included instructions, I might write an installer script one day!