Actually, I was just searching the nation here to see if anyone else had this issue before I created a post. OK, so I'm about to contact Apple on this as I've just, [almost stupidly] upgraded my 2 Mac Pros hosting the JSS and it's various components (including NetBoot) to 10.8.5 from 10.7.5. I also use link aggregation and have experienced the exact same issue. From my basic research it seems that "server.app" apparently didn't recognize link aggregation until the current version 2.2.2 (At least that's what the documentation says).
I;ve traced this all around the internet and the best I've found was a posting in German that stated that the German version of server.app 2.2.2 was indeed working. I rebuilt my main JSS server from scratch to see if this would help solve the issue and it did not. While link aggregation works for all services NOT being controlled by "server.app" it still doesn't work for NetBoot. Strangely the fileshares work properly though.
Do you have any other services that are or are not functioning through link aggregation?
