Bizarre behavior. MIDI bug?

I am step recording 16 measures part with 3 note chords whole notes. Simple operation. The part consists of 2 almost identical parts 8 measures each, with one chord difference in 15th measure. So I copied first 8 measures in to measure 9, then deleted noted in measure 15 and replaced it with different notes. Now it does not play measure 15. I am so frustrated! How can it remember that I deleted something there? Ok, so you would think- the reason is because part 2 was a copy of part one, so I changed notes in part 2, and here it goes. Bug, but ok. So I deleted the entire track, started new track did not use Copy. Just step recorded those chords again- all 16 measures note by note- no copy/paste. It still does not play 15th measure.
 
I should note that the issue persists with software synth playing the sounds. I am using Spire Pad.  When I use Yamaha hardware synth, all notes playing as written. But that does not make it any better. What can cause Soft synth not to play 15th measure (located far in to the song- it actually measure 80)?
 
Now check this out: earlier this week I was and still am frustrated with Izotope Beat Tweaker drum synth. It is probably not related to this issue, but it misses parts when it supposed to play. And strange thing- it happens every 15th measure. Some what different scenario. I have 2 instances of Beat Tweaker (BT). How does it work? Long story short- it has patterns and individual notes trigger individual patterns. I have 2 instances of BT open. First instance has 14 measures long note holding for the pattern to last, then at 15, note changes on another track with another instance. Well- that note is not playing every other time, so 2nd instance of BT remains silent. But this issue is NOT in the same location that the Spire Pad issue. Now I am thinking- there is a chance I entered the notes to BT tracks via Piano Roll and possibly deleted a note and then inserted another note.
 
This is weird. I contacted Izotope and sent them the song. The say- they can not reproduce my issue and all note playing. That was before issue with Spire. They say to test BT in VST 2 and VST 3 mode and see if it persists. I think I am using VST 3 this time. Also in case of BT, it happens every other time. With Spire track, it misses that measure every time. After I deleted it and entered new MIDI notes on the new track. Spire is VST 2. Some how it does not play that one chord. What is going on? Thank you.

My "Prepare" playback is set to 20 ms, not 250. Did you mean 20 to 50 or 500?

Vlada, the default for Edit>Preferences>MIDI>Playback and Recording - "Prepare Using ____ Millisecond Buffers" is 250 milliseconds, which many people find too low.
 
I have NO idea why you would try to run at 20 or 50, or anything less than 250 (which is already considered to be too low).
 
I recommend you change that setting to be 500 milliseconds.  
 
The default for this used to be 500 milliseconds, but had been changed for one of the recent releases.  Lots of folks have had issues with dropped midi notes running at 250, so the general opinion in the community seems to be to change it back to 500 milliseconds.
 
Bob Bone