just had my 1.9TDi serviced by a non-Skoda garage yesterday and got them to put in long-life oil, change the brake fluid, etc.

I told them to set it to variable service interval. Is there a way of checking that this has been done and can I set it myself if it hasnt - I've got VAG-COM version 4.09?

You can check by selecting:

17 - Instruments

Adaptation - 10

then check the stored values in Channels 43 (max distance to next service), 44 (time in days to next service) and 45 (oil quality, ie LongLife or not).

Ross-Tech's site has detailed info on VW service interval reminders which should make clear what you need to know. You will need a registered version to access those channel and to save changes.

PS: This is the service interval info I mentioned above.

Ross-Tech: VAG-COM: VW Service Interval Reminders