Does it make the sound in the exported file as well or is it just during playback while in UTAU? If it is in the exported file, would you mind uploading an example to show?
I believe it may be an audio driver error or something along those line than something with the program itself though since the problem also appears during preview of the oto screen (which is unfiltered). Did your computer update recently? It may have something to do with that knowing Windows.