Adam,

Don't know if this will solve your problem, but here ate the shell script lines I use to establish fixed mount points for the thumb drive that contains my Optware and other command-line software:

UUID_OPTWARE=$( blkid | grep 'Optware' | cut -f4 -d'"' )
DEV_OPTWARE=$( findfs UUID=$UUID_OPTWARE )
mount $DEV_OPTWARE /opt

These script lines will dynamically identify and mount any drive with the label "Optware." You need to wget, unpack, and copy blkid and findfs, which are not included in the Pogoplug builds to /usr/sbin and /usr/lib to make this work.

You may need to add a delay at the start of your script to allow the USB device and systems software to finish initializing.

This is what I've done to my boot procedures.

I added a single line at the end of rcS:
/etc/init.d/startOptware.sh

And a script in /etc/init.d/startOptware.sh that mounts my "Optware" drive after waiting for 15 seconds. If the drive is found and it mounts it and starts a supplemental rcS script located on the Optware drive. That way if I make changes that "brick" my Plug, I can back them out by pulling my Optware drive out and doing a cold start:
#! /bin/sh
# Load and run Optware functions:
# Locate and mounts a drive labeled Optware
# Wxecute /opt/etc/init.d /rcS_opt.sh

# Delay needed before USB drives can be detected.
sleep 15

# Get Optware drive UUID, use the UUID to get the device, mount at /opt
UUID_OPTWARE=$( blkid | grep 'Optware' | cut -f4 -d'"' )
DEV_OPTWARE=$( findfs UUID=$UUID_OPTWARE )
mount $DEV_OPTWARE /opt

# Rotate logs on Optware drive
rm /opt/opt_log.old
mv /opt/opt_log /opt/opt_log.old

echo "$(date): Optware drive mounted. Current mounts are:" > /opt/opt_log
mount >> /opt/opt_log

# Start the Optware/supplemental boot script if it exists.
if [ -f /opt/etc/init.d/rcS_opt.sh ]; then
echo "$(date): Starting rcS_opt.sh Optware script" >> /opt/opt_log
/opt/etc/init.d/rcS_opt.sh
else
if [ -f /opt/opt_log ]; then
echo "$(date): Optware script //opt//etc//init.d//rcS_opt.sh not loaded (not found)" >> /opt/opt_log
fi
fi

I was having the same problem. I grubbed around for a while before finding this thread that addressed it:

http://www.pogoplugged.com/forum/thread/17497/Problem-with-optware-and-reboot