I was having a similar issue, so I switched to the WinRT MIDI Driver and system timestamps, but to no avail. After some investigation I discovered that I had inadvertently changed the velocity curve in my keyboard at some point, causing Note-Ons at velocity 0 to be transmitted at the lightest dynamics of playing. While recording, these notes just wouldn’t register, however when stored in the retrospective record buffer they would be interpreted differently as either slight stutter notes before a longer held note, or extremely long held notes that extend for a while, overlapping other parts of what was played. For me, changing the velocity curve has thus far eliminated this issue.