I think I have solved this problem. I also noticed this issue with an earlier version, upgraded, and found it the same. So after reading this thread I decided to try a few new ideas, and one works.
The issue seems to be the 'resolution' of midi. So, if you start with a tempo of quarter note = 100, the casual user will not notice any problems when recording music. However, if you play fast enough problems pop up all over the place. The easiest way to test this is to record in a trill, start the trill slowly and gradually build speed. If you execute this trill fairly well, and play it back, you will see it starts okay, and gets off as the speed increases.
So, the problem is that with 100 beats per minute, it only gives x number of subdivisions to each beat. But you can get a much higher resolution, simply increase the beats per minute. The maximum seems to be 999, I tried that and it works great. But you will quickly run out of measures, so in the flexi-time options increase the total bars to its maximum (again 999 I think). If you still need more, change the time signature from 4/4 to 126/4 (again the maximum). This will give you the highest MIDI resolution possible (as far as I can tell). One thing to note, if you do this, make sure you also change the default of 1 introductory bar to 0, when recording in flexi time. Also you might want to switch to panorama mode for viewing.
If you don't believe me, try this- set the intro recording number of bars to 0, then change the tempo to the minimum, 4 beats per minute. Now try to record in a trill and see what happens! Even if you aren't a pianist you'll see how bad it is.
Hope this solves your problem, and thanks for starting the thread so I could finally figure this out for myself!