If your credit report shows no recent activity on any of your existing card accounts it is common for Citi to decline the application. The activity that they can see is accounts closing with a balance. It's fine if you then pay off the balance in full to avoid finance charges, but if you pay before the statement closes and they all report a zero balance Citi sees only dormant accounts.
I have all my cards set to autopay full balance upon payment due, the timing should be fine to where it counts....I would think. I also am pretty sure there is a balance at any given time, so when they pulled the report there was likely a balance on each card, even if small.