Discovered that when I have 2 Pro-site powered multisite installations pointing to 1 Stripe account that the plans would overwrite each other so I could only ever have 1 site's plans live at any one time.
I looked at the code in gateway-stripe.php and found that for both sites the level name was the same. pro_1
I therefore on one of the sites edited gateway-stripe.php to give a level name of pro_xx1, pro_xx3 and pro_xx12.
Fastest way to do is search for: "_1" (include the speech marks) and then edit the line.
Anyways the end result is I have 2 separate Pro-Site installs running and syncing their plans with Stripe with ZERO conflict.
@Aaron perhaps an extra setting for stripe to set the level prefix for plans might be worth adding in the future?