Perhaps the Due built StandardFirmata isn't sending the proper capability data for firmata_test to detect the number of pins and their capabilities?
I've uploaded a couple builds of firmata_test for Ubuntu 12.04, one with the logging window enabled. Perhaps if you try that, it may give some more info about what's wrong. If you don't see the log, try moving the main window. It might be underneath. The log window has a menu that lets you save all the info to a file, to make it easier to share the results.
The only documentation on firmata_test is its source code. To see what those log messages mean, look for the printf() statements!