Clarification: Is the "my openacs-4.6" you talk about here:
> To achieve this I did a cvs import of my openacs-4.6 like this:
> cvs import -m "Service on OpenACS 4.6" service OpenACS openacs-4-6
your "modified" version or a clean 4-6 from tarball/CVS?
If it is indeed a clean version, then I believe your approach should work, using the "-j openacs-4-6 -j openacs-4-6-3" variation (the spaces was lost in your posting, but I believe they are needed)
If not, then you miss a "common ancestor" for the two versions you have. The merge involves THREE versions of the code. You want to merge the changes from 4.6 -> 4.6.3 into your version, so all these three versions need to be in CVS.