Hi Julius,
Were you able to solve the problem? I have a similar issue.
When I add a table, I do not see the any check box for R/3 adapter. It is present for indiviual fields. That also is not needed as per note 1287948 - R3 adapter flag for account enhancements
Also I have a typical problem, when you add a table using AET, for BDoc mapping some FM are generated locally. These may start with names /1CRMGC/*. In our system, some AET added tables are present in these tables, some are not(these are the ones I created). AET generation was successful. Do we need to add code manually here? I seriously do not think so. It should get generated.
Also had a look at Txn AXTREG. Did not find anything suitable there. You could be helpful to me.
Thanks,
Niraj