i've had this problem before, its a glitch really, i don't know why, but what we ended up having to do was actually make the guild public before the person i invited could get in, i was lucky i had the access to do so..
otherwise you will probably have to email support about it. because it is a glitch, my friend tried with her spare account, but for some reason couldn't get in with her main.
but this was before they had the guild upgrade, so it might be a bit different, but it sounds the same, so it might be
good luck!
If you see my sanity, get it to give me a call.