Mark,
It was not for my own use, I was responding to a possible requirement mentioned in other threads. But thanks for the information, it may help to guide my design.

I am planning a utility which reads MIDI and writes an updated MIDI so that users do not need any extra software.

I am already aware that simple quantising is not the answer, and had established that it is the shorter notes which are the problem. I do have an idea of what to do, but it may need parameterising to be compatible with different scoring programs.