Yes, the positioning of the adverb "entirely" can change the meaning of the sentence slightly.
In sentence A, "entirely" modifies "not a bad thing," indicating that the speaker thinks the thing is mostly positive or at least neutral, rather than completely negative.
In sentence B, "not entirely" modifies "a bad thing," suggesting that the thing has some negative aspects, but it's not entirely negative.
In sentence C, "an entirely bad thing" is being negated by "not," indicating that the thing has some positive aspects, but it's not completely good.
Therefore, even though the overall meaning of the sentences is similar, there are slight differences in emphasis and implication depending on the placement of the adverb.