I've tried a billion different ways to ensure we're reading in all the data. At first, I was just asking the usb stream to present me with a certain number of characters, b/c that's how all the examples do it.
But we're using a lot of different cards with the readers, so that didn't work too well. So now I just read one character at a time until we find the new line.
Here's the code to find the device, open it, close it and read from it, all whilst finding and converting the data as required.

So using this code, we take the swiped data and send it to our server for storage.

Anyway, like I said, great when it works. So I'm working in linux which basically leaves me having to use java libs and a shared object file.

Here's my code:

It sits and waits until the sig pad gets some points on it. Once we have points it waits for a lapse in time where there is no change in the number of points.
Once we've decided that we have captured a signature, we store it to a file.
Then we shell out to a ruby script - see the httpi and curb article - which is how I get the file to our rails server for display and verification from the user.

Now, you'll need a few files. Most of which can be found in the java zip download from the vendor site.
From that zip, you should grab the following:
SigPlus2_60.jar
RXTXcomm.jar
libSigUsb.so - if you need the 64 bit version, go here - http://www.topazsystems.com/Software/libSigUsb7242012.zip

Then I just used eclipse to set everything up and build. Works well so far.
The only thing you may need to change is the model (I have mine set to SignatureGem1X5) and com port (I have mine set to HID1).

svn checkout http://azilink.googlecode.com/svn/trunk/ azilink-read-only

Step 2 - Update the UdpDriver.java per this azilink issue.

Step 3 - Build and install the apk

# this will give you a build.xml file
android update project --target 2 --path /path/to/your/azilinkdownload/
# after plugging in your device and from your azilink project directory
ant debug install

Step 4 - Install Open VPN

sudo apt-get install openvpn

Step 5 - Grab the azilnk.ovpn file from the downloads section.
Place somewhere you won't lose it.

Step 6 - Copy this resolv.azilink file to the same place as the azilink.ovpn

Step 7 - Copy this azilink script to somewhere you can get to it

Step 8 - Start azilink on your phone.

Step 9 - Run the script from step 7.

That's it.

mount /dev/sda1 -o rw,remount

Now that the drive is in read-write again (test with a simple touch /tmp/test), continue the installation with this:

dpkg --configure -a

For those having the same problem, this is where I found the solution you see below.

$ sudo sdparm --clear STANDBY -6 /dev/sdb
# note that your device could be something else, for example - /dev/sd<something>

And if you get an error, something like this:

change_mode_page: failed fetching page: Power condition

Then you should be able to use hdparm instead, like this:

sudo hdparm -S 0 /dev/sdb