The following is an email exchange between myself and the support department of PDF995, .. I think it sums up the problem fairly well:

----- Original Message -----

From: Jose Guia

To: support@software995.com

Subject: PDF995 and Long File Names

Hello,

 We are having issues with PDF995, when I do a silent BATCH plot using a directory with a long path our pdfs are not plotting and are instead being over-written by each other to a set folder with the name “.pdf”

  Is there an INI switch to force it to use SHORT FILE NAME ?

  Jose

 

 -----------------------------------------------------------------------

Jose,

 

This following indicates that document name that the windows printer system is passing to pdf995.

Document Name=T:\Directory Where we Store a Bunch of Stuff\ST\NO ADDRESS.NO ADDRESS\01.11111.00-Fancy name of a fancy project\Design\Arch\DWG\CD\A\011111100-Current Phase of Project\

We cannot control this. You need to use a shorter file path. Otherws, pdf995 cannot determine the name of the file.

Thank you,
Software995 Support

So after a bit of googling I came across Robin's blog entry about an AutoCAD variable I hadn't known about, "FULLPLOTPATH" 

http://rcd.typepad.com/rcd/2005/09/seeing_the_plot.html

Seeing the plot with AutoCAD 2006

It won’t help you figure out “who done it” in the thriller you’re reading but I found an AutoCAD variable that will let you see the plot.

If you have a plotter with a small on-board display, like our HP 800, AutoCAD’s recently acquired habit of sending the full path of the plot file to the printer can be rather frustrating. You see an endless list of truncated paths but can’t see the filename.

AutoCAD 2006 “fullplotpath” variable toggles between sending the full path or just the filename. This makes reprints from the plotter and cancelling other peoples plots, so yours come out faster, much easier.

Command: fullplotpath
Enter new value for FULLPLOTPATH <1>: 0

0 Sends the drawing file name only, 1 Sends the full path of the drawing file