The radius of the bootstrap circle depends on the bootstrap value itself, on the length of the branch from the node towards the tree root and on the configured zoom factor/limit.
For a zoom factor of 1, a bootstrap value of ~44% will show a circle/ellipse which completely contains the whole branch.
Such a bootstrap value indicates a certain fuzziness and the associated bootstrap circle attempts to graphically visualize that fuzziness.
Branches covered or overlapped by circles can be considered more or less unstable.
For increasing bootstrap values the radius goes towards zero; for smaller bootstrap values the radius will get infinite  that is why ARB uses a 'Bootstrap radius limit'.
The formula used to calculate the (unlimited) bootstrap circle radius is
(1/sqrt(bootstrap/100)  1) * 2*branchlength
