YDL corrupted on G5 dual-boot machine after reboot

[Sanjay Bhatnagar]

Hi,

I installed Mac OS and YDL on my desktop G5 machine.  Mac OS partition
was the last on the disk and the free-space was used for YDL
installation.  After installing YDL, and booting the machine in Linux,
all worked just fine.  However after I re-booted the machine in Mac OS
(which also worked fine) and then back into Linux, YDL did not boot
well.  All of /var is gone and it complained about various things
failing while booting.  It ultimately cannot start X and comes with a
an error message saying:

 Sever Authorization directory (daemon/ServAuthDir) is set to
/var/gdm but this does not exist.

This is the second time this is happening (after the first time, I
reinstalled YDL).  Can someone help and tell me what's going on and
what I am doing wrong?

Regards,
sanjay