This has happened to me frequently since guild store mails started appearing instantly.

For me the inbox shows as blank (even though I have old mails as well as new mails) if I buy something from a guild store, retrieve it from mail, and buy another thing from that same zone. It seems the system where you can force mail to pop once (in a given period of time) before needing to switch zones is still in effect. The blank mailbox can also happen if I check my mail immediately within the first few minutes of logging in, where it seems the mail hasn’t loaded properly yet, and less commonly in other circumstances.

Switching zones and waiting a few minutes usually fixes it for me, and relogging will fix it as a last resort, but that also contradicts the whole idea behind guild store mails supposedly arriving immediately.