Dominant male hates his daddy!

My 1 year old neutered Male Lionhead/lop mix Clive bangs his feet loudly and runs off whenever my partner steps into his pen or even opens his hutch! However he has only just started doing it and is absolutely fine with me. My partner is the one who did all the bonding work recently between him and his bun friend Betty. Bonding went well though. Fair to say my partner gets a bit upset about How Clive reacts to
Him

Just like any relationship, development time can vary. Especially since your rabbit developed a bonded mate, it makes sense that he may reassess who are his secure supports versus not. Anecdotally, my male rabbit (neutered) favored my partner first, as he interacted with him solely when we got him (he was a surprise gift while I was gone on vacation); then, tables turned and he ended up loving me and being intolerable of my partner. Eventually, my partner just realized that he needed to start over from square one. It's unfair that that needs to be done, but the relationship between a human and rabbit can be complex because we cannot communicate directly.