[bitesize]

Have you googled the pill to try and gain a better understanding of it?? it might help put your mind at ease, if not with this situation, in the long run. Personally I don't think it's a great idea that she's skipped her period three or four times now, but I don't have any experience with this and don't know much about it so maybe it's ok.
If she's been taking her pill every day and hasn't thrown up/had diarrhoea/been on antibiotics, there's not really much chance that she's pregnant. The pull-out method is not an effective form of contraception alone, espcially because of precum, etc, but as the pill is 99% effective I think you guys are probably ok. Of course there's always a possibility, but I really think if the test came up negative things are ok. Maybe you could wait another couple of weeks and take another test just to be sure..??