All items are truly there, this is part of the guild bank bug introduced with IC.
A work around I have found is to log out and login again. Thus grants you ONE SHOT to access the guild bank in question, deposits and withdrawals. You might even have to drop guilds to make sure this guild is the FIRST in your list. After doing this, I never have problems with my first guild bank access after login.subsequent attempts on same login session show either no items or a fraction of what is there.
It's still an arse pain and the biggest problem with ESO arm imo.