Just after posting this I did an upgrade on my machine and there was an update to udev. After applying this update the auto mounting works fine for my IronKey.
So if you are experiencing this issue and if its possible upgrade your system do so. Make sure you have udev version 162-2.1 and it should work fine again.
If you still have issues or if your unable to upgrade the method below should still work fine.

Recently I finally got myself an IronKey and have been using it just fine under Ubuntu 9.10 and 10.04.
But after upgrading to 10.10 I have found that it does not auto mount the disc that contains the Ironkey software as it should.

After a bit of research I worked out the simplest way to mount the disc manually is to do

udisks --mount /dev/sr1

This works fine mounting the software under /media/disk/

You can then just run the software by doing

sudo /media/disk/linux/ironkey

There is an open launchpad bug for mounting hardware encrypted usb stick failes hopefully this means the issue will be fixed soon. Just thought it was worth giving everyone a heads up on this issue in the mean time for people who encounter the issue.