what's in the logs of the other server? Does it look similar?
802.3ad between two Linux servers, directly connected, should work (as long as you have only a single bond per server - there's no way to set partner IDs with Linux ).
There's a lot of ups & downs of the interfaces going on during boot - I take it that's caused by setting the interface parameters. This happens after bonding the interfaces, maybe that's confusing the bonding driver?
I suggest that you start both servers from a Linux boot medium and try to set up the LACP link manually. That way you can confirm that it indeed works and can spot potential pitfalls.
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