Thanks Marmad. I gave it a go, but the results weren't particularly conclusive. I'm probably doing something wrong, I assumed that by feeding in a 40MHz siginal to trigger it, then I would be able to trigger it every time. But I get different minimums depending on whether it's 40MHz or 35MHz.
Anyway, I think for the DS1000 series I've probably put about as much effort into this one as I'm going to. I've got some reasonable results, I know that above about 40 wfms/s it'll start dropping the odd trigger (which is what I saw in the original method.)
The trigger out on the other hand could be worth putting some time into. I don't think isolation is needed, as for anything I can think of it'll be triggering another mains earth reference device. But a high speed 50ohm driver would be a definite requirement. But yeah, that would need to go to the end of the list of other projects I've got on the go at the moment.