Why are duplicate method suggestions appearing in Eclipse?

You have Code Recommenders installed. The proposal with percentage is coming from that, and the proposal without the percentage is coming from JDT.

Essentially there are more than one completion engines installed - see Preferences > Java > Editor > Content Assist. The same method is being offered by more than one engine. While this explains why the duplicates are there, I do not have a workaround or a solution in mind.

Go to Preferences -> Java -> Editor -> Content Assist -> Advanced

To see no duplicates in your suggestions, have the assist list checked as shown below.

(Tested in Eclipse - Kepler Version)

If you have checked "Java Type Proposals" and "Java Non-Type Proposals" then you will see duplicates in your suggestions.