I'm not sure what it could be. I would see if you could get in to see your doctor. I am in the middle of a really weird cycle too. If I don't get AF next week that will be my 2nd missed. I had seen my doctor 2 weeks ago but she said they won't run any test until I've missed 2 AFs. First time this has ever happened to me. I have never been late before last month. Doc did a Quantitative blood test and my hCG was under 5 so I know I'm not pregnant. Have you tried another hpt recently? Maybe you got pregnant before your 2nd missed AF? I hope you get some answers soon hun and that everything is ok. Good luck!
If you are getting negative hpt maybe it's a hormone issue or stress. AF can be very sensitive to stress, hormones and even weight gain or loss. I'd call your OB/Gyno and get an appt. Good luck!