For starters, I do not know what differences there are.
I do not use docking, nor do I have the getlazarus version. So I can only give some guesses.
Maybe they ship an svn version? That is between the official releases, changes are added to svn. Anyone can download those changes. So they could build a release with all those changes.
Note, that 2.0.6 only contains selected (safe fixes) changes. So the total changes start from 2.0.0.
Maybe they have even some patches of their own. IIRC they contributed in the past. So then maybe if they have own changes they will contribute again.
Maybe it is just a configuration issue.
I can only advice you to clearly describe the differences you are looking for.
If they are config, someone may know.
If they are not config or if they are crashes or bugs (in which case config does not matter), then do report them on the tracker. (search first, if they already are there)
If no one reports bugs they will not get fixed.
Afaik that is especially true with Anchor docking, because it may be that none of the core team members uses it in their own setup (I don't that know for sure). So then core team members may never notice until they read a bug report.