Two thoughts come to mind:
Are you accepting the transactions or otherwise marking them as fulfilled? It's been a while since I've sold items through Square's online store feature so I forget if this is needed for it, but I know many online store management systems require that you verify or mark an online sale as being fulfilled before the funds will be passed on to you.
Also, setting up instant deposit doesn't mean the funds instantly come to you when a transaction is completed. It only means you will have the instant deposit option made available to you, through the Dashboard. You'll still need to go into the Dashboard and choose to send the funds via instant deposit (1% additional fee) each time you want the funds sent. Otherwise they'll just be sent in about one business day. I do not believe there is a way to have instant deposits occur automatically.
