Maybe look a little bit harder. In the 1990s the Baltics each saw a majority vote for pro-independence parties. Each of the three states organised a referendum on independence, and all three voted in favour (by 77%, 78% and even 90+% in Lithuania).

The march 14th 1991 referendum you're probably referring to was not held in the Baltics. Additionally, it is often framed as a vote against independence, but that's not really what was on the ballot in the first place. The referendum was on the New Union Treaty, and was phrased as:

Do you consider necessary the preservation of the Union of Soviet Socialist Republics as a renewed federation of equal sovereign republics in which the rights and freedom of an individual of any ethnicity will be fully guaranteed?

Emphasis mine. Note that the alternative in this case was the USSR continuing as it existed before, meaning there was no vote on the dissolution of the union. The majority voted in the direction of more sovereignty for the constituent states, the closest thing to independence on the ballot.

Pro-Soviet groups in the Baltics did attempt to hold their own independence referendums, but none managed to reach a 50% turnout and they were boycotted by the Baltic Supreme councils.