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).