Hi Icelander .

Do you have Melodyne ?
Melodyne does an excellent job of converting audio to midi without the glitches you comment upon , plus it does so many other valuable tasks as well..., just an alternative suggestion .

I would also hit up support as the other comment mentioned to report that bug you commented on, and hopefully that hiccup could then be logged ...., then worked on and hopefully recitfied ASAP


My Specs
Computer : Mac Pro (late 2013) - OS Yosemite 10.10.5
Processor : 3.5 GHz 6-Core Intel Xeon E5
Memory : 64 GB 1866 MHz DDR3 ECC
Graphics : AMD FirePro D300 2048 MB
Interface : Avid Mbox 3 Pro
DAW : Pro Tools 12.6.0 (64 bit AAX)