I'll keep prodding away at it and post up my findings.
I created a VERY basic SPD workflow that just ended itself and logged to the history. That sits at starting for AGES, then finally kicked off. But the real one wont fire passed starting. It manually starts as I said though so I doubt it's broken.
There's no initiation on it either, so no need to pass in data as far as I can see.
I'm not sure if there's any mileage to be had in getting the workflow object that is created on the startworkflow event being fired. I've had a look and there doesn't seem to be much on offer from it unfortunately.
It's just a simple email out some details workflow from SPD, so worst case scenario is just coding it into the timer job. But I'd rather keep it as a workflow because then I can let our business change guys go in and do the pointing and clicking to update any bits of the WF they want. Plus it'll make good sense to get it working now then document it for possible later use.
However, if I don't come across any solutions by 3pm then it'll just have to wait as I'll be out of here as I've got a well earned week off!