The page always defaults this way, and shows the differences between the 2 branches once their has been activity. You can change the top level branch, and then the comparisons below will change to show the branch you are on compared to the top level branch you just selected.
This page is intended to be completely separate from the 'create branch' page/feature, and is not actually representing the architecture of your repo, and branches. The branch you originally created is still branched off of the branch you set, and should be represented when you look at the tree locally.
Did you actually try the steps from Gideon? It seems clearly wrong to me and it is a problem recently introduced - it has not 'always defaulted this way'.
The branch 'Tes01' in the case above was off 'second' but reverted to 'master'.
Whether the pages are separate or not is irrelevant. If I say 'create branch3 off branch2' when I look at branch3 the source branch should not have changed to branch1. And I does change.... you check out branch3 and its off branch1 not branch2
@glynjones - I have tried the steps, and this functionality has never changed. Remember, a branch is simply a lightweight movable pointer to a commit. Once you create a branch through the ui, it is empty, and does not belong to any commit until you checkout and push back to Bitbucket.
However, that being said, I definitely can see the confusion for an end user if you did not know how we intended this to work, and the panic that it could cause. I am going to reopen this as an improvement request, and have our PM review. Feel free to drop any more feedback here, or ideas on how we can improve this feature.
Apologies for the delay in getting back to you, and for not giving this enough attention.