After a re-boot, my C3100 running pdaxii1v2 now no longer mounts the microdrive.
Did you have 3 partitions after you first installed pdaxii13 ? 
(one ext3 for programs, one for swap, and one vfat for FAT) 
Or to rephrase my question, 
Did you follow Meanies instructions when first installing pdaxii13 about formatting the drive during the installation setup.
If you had a "GOOD" setup after first installing pdaxii13, and now your partitions have "disappeared" after using pdaxii13, I am sorry I don't have an answer to that particular problem.
Hopefully Meanie will see this and be able to help. I would think the mounting of the hard drive on boot would be handled the same or similar as in pdaXrom beta3.
Sorry, I didn't read the entire post when I first replied.
The partition manager shows 3 partitions (type 83, type 82, type c) as I originally created them.
So I'm guessing that the microdive is ok, but the process that mounts it on boot is broken.
What is the "partition manager"? Is that in the setup screen? (I haven't re-flashed in a long time and have forgot the choices in the setup screen.)
If you decide to reflash, make sure you follow the instructions carefully when it comes to partitioning the hard drive. It can sometimes be confusing because, over several version changes of the installer, the prompts for formatting and partitioning the hard drive have changed. 
Below is "mount" and "df" commands on my pdaxii13v2 C3200. (Note, I leave my 1GB CF (hda1) inserted at all times, hence the hdc1 and hdc3)
root-:) mount
rootfs on / type rootfs (rw)
/dev/root on / type jffs2 (rw)
/proc on /proc type proc (rw)
none on /dev type tmpfs (rw)
/dev/hdc1 on /mnt/ide type ext3 (rw,noatime)
/dev/hdc3 on /data type vfat (rw,noatime,nosuid,nodev)
none on /dev/pts type devpts (rw)
/dev/root on /mnt/user type jffs2 (rw)
/dev/mmcda1 on /mnt/card type vfat (rw,noatime)
/dev/hda1 on /mnt/cf type vfat (rw,noatime)
root-:) df
Filesystem           1k-blocks      Used Available Use% Mounted on
/dev/root               123904     95404     28500  77% /
none                     12288        16     12272   0% /dev
/dev/hdc1              2115276     76808   1931016   4% /mnt/ide
/dev/hdc3              3593540    139428   3454112   4% /data
/dev/mmcda1            1979828    428084   1551744  22% /mnt/card
/dev/hda1              1013028    668184    344844  66% /mnt/cf