Yep, it's too soon. All the home pregnancy tests i've seen say in the instructions that they can't detect prenancy until after you've missed your first period. Even blood tests available at clinics take two weeks after intercourse to show a positive result. At least you have one negative test, though. I'd wait a week, and test again. You could also consider going into a clinic for the most reliable results.
It is possible you're pregnant, so i'd definitely get a test done in a week, but it's also quite possible that you're just spotting. Birth control pills can have a significant impact on your period depending on your body chemistry - some women even go on them because it forces their body to regulate. For me, the pill's effects also changed as I aged.
It's great that you didn't stop mid cycle, and you won't know for sure till you test - but i've had several scares when I had strange bleeding, or no bleeding at all, and it turned out it was just new side effects of the pill. Trying not to stress, and looking into a birthcontrol more suited to your lifestyle is key now.
If the pill works well for you chemically, you might consider the nuvaring. The nuvaring is very similar to the pill, but it goes in once every three weeks and just stays there- I liked it a lot because I only had to remember it once in a while, despite a crazy schedule, and I could mark the important date on a calender with a sharpee. It couldn't come off, and internal fluids or swimming don't affect it. You can also stop it at any time. For a hormonal, it was great. The patch has similar benefits, and both allow you to get your period monthly to 'prove' you're not pregnant.
Keep us posted. Good luck!