If you have 90 bushido and try to bond your bird, you may see messages saying that your bushido skill must rise before it can bond, etc. I am pretty sure this is a result of the same system that causes commands issued by a 90 bushido char to fail a lot. They set 90 skill as a minimum skill to be able to deal with the birds, and it's kinda a mess.
To overcome this and succesfully bond your bird, keep feeding the week-old pet, dump piece after piece of meat on it and ignore the complaining messages about bushido being too low. If the correct time has passed, it should bond up on one of those feedings. Give it at least 10 pieces of meat before giving up.
If it doesn't work after that, try later in the day or tomorrow. I've seen pets bond not at server up but a bit later, after I'd had the pet out a while and was doing things with it.