The tradition I have in the name of the Rav (Rabbi Soloveitchik) is to say the Omer twice (but obviously with only one B'racha at the beginning), once with a Bet and once with a Lamed. The reason for both pronunciations is to fulfill both side of the question as to whether Sefirat HaOmer is one Mitzvah or fourty-nine separate Mitzvot. Saying B'Omer implies there are fourty-nine separate Mitzvot within the Omer period. Saying L'Omer implies moving toward a goal which is the fulfillment of the one Mitzvah of counting, only completed when one has numbered all fourty-nine of its days.<br>
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Kol Tov<br>
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