Makedepend does not accept the -Y option. If you compile
XFree86 4.0.2 that version works correctly.
This could be a command line parser problem ?
It looks fixed in 4.0.2 and 4.0.3. If you still find a problem
though please reopen the bug.
Same bug in RH7.1 and XFree86-devel-4.0.3-5,
makedepend -Y outputs: Unknown option '-Y' ignored