First, try to find out if Epson's software will tell you which cartridge it thinks is empty.
Go to Start > Control Panel > Printers/Printers and Faxes; right-click on the Epson printer icon and then left-click on Printing Preferences. Click on the 'Maintenance' tab. Click 'Epson Status Monitor'. Hopefully that will show which cartridge is the cause of the problem. (I've not got an Epson printer, so I'm not sure as to exactly what you'll see there).
Epson print cartridges have a chip, which monitors the ink level. If you've inserted genuine (but pricey!) Epson cartridges, there shouldn't be a problem (unless the cartridge was made with a duff chip). However, if you've used cartridges supplied from elsewhere, they're probably recycled cartridges. The manufacturer should have reset the chip to indicate that the cartridge is full but, if that's not been done, there's the cause of your problem.
Chris