Reb Shmuel suggested that there is another type of sifek sefeika. This type does not work by creating a majority of the possibilities that point to permitting the issur. Rather, this type says that if so many steps must be taken in order to prohibit this scenario, it is unlikely that one can assume that the issur occurred. In this type of sifek sefeika all of the doubts stem from one ultimate safek; however, if that one safek is so far removed, we do not have to be chosheis for it. Rashi, in Baba Kama 11a, uses this idea to explain the sifek sefeika in that Gemara.
We can suggest that the sifek sefeika of the Rama is the second type of sifek sefeika. Therefore it is not a problem that both of the sefeikos are essentially one safek. This is because this type of sifek sefeika holds that we are not worried that the many necessary steps that had to be taken in order to prohibit this scenario occurred. In this case we would say that we are not worried that the grain grew this year because: 1) perhaps it grew before the korban omer; and 2) even if it did not grow before the korban omer, perhaps it took root before then. Since two steps had to be taken in order to prohibit this grain, we rule that it is permitted.