Oto.ni not compatible with resampler?

Try selecting one of these problematic notes, press ctrl+y, a window will open that will have red lines and red lil squares. Check if those squares dont have another square below then by moving them slightly to the left or right with your mouse. If they do, separate the squares and try again

setParam isn't always accurate, it's more of a guide where to put the offset, consonant, cutoff, etc. So if it sounds bad, you will need to edit the automatically generated parameters by moving them a bit.

If the red and green lines (preutterance and overlap) are in a blue area, put them instead in a pink one. DON'T go too far though, as it may sound bad. For preutterance, put the red line where the vowel starts. For overlap, put it between the start of the note and the red line, or just near the preutterance.

It may also be a problem the envelopes, though, as Mougeki Mero said. The problematic notes have exclamation marks above it, so press Ctrl+Y and edit them a bit or maybe just reset the envelopes using the "reset" button above.