retrolefty:
Typically one could start looking with an oscilloscope to see what the Vcc voltage looks like and possibly how you have the arduino and motor ground wires routed to the negative terminal of the power source, they should not share the same conductor anywhere and be connected together only at the power supply.It can be solved but you have to have good tools to see what you are up against and what effect any changes you make have on the situation.
Lefty
it's pretty much setup like this
http://bildr.org/blog/wp-content/uploads/2011/03/tip120-solenoid.png
my power connections for the motor are connected to the dc supply, before the 7805 regulator. Maybe I'll rip it apart and start from scratch with the uno, then move to the breadboard arduino when that's functioning, Although I've done that already a few times.