This has nothing to do with octrees, it's just a problem of painter's algorithm. If two or more transparent polygons get sorted, the sorting may be inaccurate. There is no real solution to this, except for

a) modifying the geometry so that it can't happen

b) don't use so much transparency

c) apply a sort offset

c) is only possible for things that are always behind (like the skybox) or always in front.

The problem with painter is this: You sort by the average depth of a polygon (or by the depth of one of its corners...it doesn't matter, the problem is the same). Have a look at this skillfully drawn picture

Assume that the average z-value of those lines is calculated by adding the z-values of their ends and dividing by 2. The camera is located to the left in this example.

Fig 1 will be sorted correctly. Fig 2 will most likely be sorted correctly but Fig 3 for sure won't. The short line has a lower average z-value then the long line has. So it will be sorted in front where it should actually be sorted behind the long line.

As said, this is a problem of the algorithm....why is your whole map transparent?