Restoring cached option prefix=C:\msys\home\gerz\lyx-trunk-bin
...
Install file: "C:\msys\home\gerz\lyx-trunk\lib\ui\stdmenus.ui" as
"msys\home\gerz\lyx-trunk-bin\Resources\ui\stdmenus.ui"
The drive prefix "C:" is ignored.
Do you see anything related to DESTDIR? The logic is:
1. if there is DESTDIR, use DESTDIR+prefix without drive letter.
2. otherwise, use prefix.
To make sure, you can try
scons ... load_option=-DESTDIR
to clear previously used DESTDIR.
BTW, this use of load_option is kind of weird. I am changing it to
unload_option=DESTDIR...
Bo