Have to unplug the STM32F4 discovery card to update program

OK, The way to achieve communication in Atollic TrueStudio for ARM Lite (yes it works under lite wersion since 3.0):

1. Enable Serial Wire Viewer in active debug configuration
2. Show SWV Console (under Debug prespective)
3. Open Serial Wire Viewer settings (first button in SWV Console window)
4. Enable ITM Stimulus Port 0
5. Enable Start/Stop Trace button in SWV Console (second button)
6. Use ITM_SendChar function
7. Enjoy debugging strings!

I also have the Discovery board but only used it with Windows and the Raisonance toolchain (after a brief mess around with the Atollic IDE and embedded ST-Link). However, it doesn't sound to me like it's a compile/platform issue if everything else in the demo is working okay. You could try going back to your original setup to confirm this though.
One thing I did notice whilst using it was the USB connector is quite delicate (I have had to resolder a couple of USB mini/micro connectors on my own prototypes a couple of times after repeated use)

So my guess is from your description, it sounds like it's quite possibly a bad solder joint on the (micro) USB connector - try testing the continuity on all the pins. It will be hard to get a probe on there, so plug a cable in and probe at the A connector side (you may need to wrap some thin wire round your probe tip, or break the cable), with the other probe on either one of the STM32F4 USB pins, or a power/ground point (look in the User manual, it has a schematic)
If you have a scope, probe the USB pins to see if there is some activity on there (even if the scopes bandwidth isn't capable you should be able to see some activity)