This is pure guess on my part concerning Status Monitor since I do not have an Epson but if it is like all of the other printer, the Status Monitor just estimates how much ink is used since the ink cartridge was new and thus estimates the ink level. There is no way for the printer to actually know what the ink level is. If you refill the ink cartridge, nothing is done to the estimate and so the Monitor will report the ink level as empty when it is not (and then shut down your printer).
I would agree with you that the ink reset facility is causing that problem. My guess is that instead of resetting the estimate, it just removed it to keep you printer from being shut down. Is there a way to uninstall the reset facility? If so, I would think that would solve your Status Monitor problem (but it would probably show your ink levels as being empty).