Yep, my 2007 Exige S does this also and I'm not using the Stock ECU, I've got the FF EFI power package setup.
I've been told this is normal, I've been this is NOT normal. It doesn't always do it either. Sometimes it's 1500-2000, sometimes it's 3000, sometimes it's 1000. If this were a vacuum leak it would be consistantly doing the same thing every time. So I don't think it is vacuum related.
I believe the only significant input going to my stand alone EFI is the throttle position -- FF/Casey feel free to correct me.
From the rumor mill, the fly by wire throttle unit used in the Lotus (or at least in the '07 Exige) is not of very good quality -- I can't confirm nor deny this as I just don't know. But during my dyno tuning the throttle position indicator was fluctuating pretty significantly with NO one in the car. I believe Casey tried to compensate for this fluctuation -- not exactly sure how.
It will be interesting to see if the '08's have the same problem -- anyone called a Lotus dealer to get part numbers of the throttle units for '07 and '08 Exige S?
Ugh, looks like Lotus need to address this in a big way.
And please nor more BS about the type of fuel used, etc. etc. Lets get the to the real reason this is happening and IF a solution is doable.
I still maintain it is the throttle sensor or something related that is causing this problem.