Sustain pedal issue / notes end early before bar line

This score was generated in MS3, and opened/saved in MS4.

The last two notes of Meas. 16 in the bass clef sustain and are held into Meas. 17, even with the pedal going up and down on the downbeat.

The last notes of Meas. 18 stop at the "4 &" instead of making it to the end of the bar.

These bugs occur elsewhere in the piece in the same manner.

It's possible that the two issues are related.