I figured out how to solve / work around the issue:
The main problem was the weird handling of lists in EA.
First, I've created all the steps in the main flow, then I've created the alternate scenario and it's steps.
At last, I've updated the according step in the main flow - which changed the order of the steps in the list! The updated step was moved to the end of the list (as if the EA deletes, changes and reinserts the element?).
An example:
Step 1, Step 2, Step 3 are available for the main flow (in exactly this order).
After updating step 2, the order was changed to: Step 1, Step 3, Step 2
My solution is to attach the alternate scenario immediately, which means that I have to create all alternate / exception flows before I'm creating the main flow. But this way I won't have to deal with EA's strange behaviour. Perhaps there's something I still missed and another, more viable, option is available. But on the other hand nobody answered my post.
Just hoping I could help somebody else who stepped into that trap.
Thanks for your help.