Starting your store with an order # like 100000001 does not inspire a lot of confidence in a customer, IMHO. To fix this the easy and safe way go to app/code/core/mage/eav/model/entity/increment/numeric.php.
Within this little file you will find the following code on about line 50:
$next = $last+1;
The “+1” indicates how Magento will come up with the next order number. So guess what we’re gonna do........give up? Ok, replace the “+1” with “+3424” or substitute ‘3424’ with some other random number. Now upload this to your Magento store and clear the store cache. Next, place a complete order through your store (that means pay for it and everything). Doing this you will find that your order number is now whatever your last order number was +3434, or whatever you’ve chose. Now go back into the numeric.php file and put it back the way that it was, to +1.
It works fine for me running multiple stores v.184.108.40.206
This is a very simple thing but I had to hunt to find it. There were forum posts requesting help completing this, usually the advice was to change the last order ID in the database.