create a new file, or rename an existing one, using konqueror, and put a % somewhere, i.e. call it "100%.txt" the name "100%.txt" appears. but, open a terminal and do "ls".... you see "100%%.txt" do "mv 100%%.txt 100%.txt && ls" you see "100%.txt", while there is no difference in the konqueror window.
This is an upstream issue and should be filed at bugs.kde.org.