In addition to @Marek’s comment about not including fixed==TRUE, you also need to not have the spaces in your regular expression. It should be "A1|A9|A6".
You also mention that there are lots of patterns. Assuming that they are in a vector
toMatch <- c("A1", "A9", "A6")
Then you can create your regular expression directly using paste and collapse = "|".
matches <- unique (grep(paste(toMatch,collapse="|"),
myfile$Letter, value=TRUE))
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