I looked over a list of acronyms just now and found many examples. OK, they are not the first letter, but still...
the s in laser (stands for "stimulated", but pronounced like "z" instead of like "s")
the u in scuba (stands for "underwater" but pronounced as a long "u" instead of short "u")
the s in taser (stands for "swift", but pronounced as "z" rather than "s")
the o in awol (stands for "out" or "official", depending on your view, but pronounced as "ah" rather than "ou" or "oh")
the a in swat (stands for "and" but pronounced as "ah" rather than short a)
In fact, it seems to me that once an acronym has become a full-fledged word in English, it is typically pronounced the way it looks in English. Can you think of examples to the contrary, where an acronym which has become a word is pronounced *differently* than it would had it been formed as a regular word, due to the underlying words in the acronym?