I'm glad you managed to reproduce it. I'm surprised no one else has noticed it before. I had noticed it happening in X2 as well although I didn't use X2 much as Samplitude is my main DAW and only briefly tried IQ . But I upgraded to X3 as I thought I would try learning it seriously and Input Quantize is something I use a lot in Samplitude so that's why I discovered the problem. Thanks for you help.

Are you going to submit a bug report or shall I?

OK I sent in a bug report plus an auto merge FR.

Do you think there's a chance that auto MIDI merge will be in X3e? I'm really finding the lack of this a a huge drawback in using Sonar for midi.
 
Cakewalk seem to have acknowledged the input quantize problem so hopefully that will be fixed at least.

I doubt "auto-merge" will be introduced since that would be a new feature as opposed to a bug-fix, but based on the recent attention given to the Input Quantizing issue and other loop-recording related issues on the forum, I think there's a good chance that gets fixed this time around.
 
But I still don't get where the lack of auto-merging MIDI takes is a real showstopper. With all the other time and effort that goes into composing, recording and polishing a MIDI performance, tweaking patches and processing the synth output, taking the time to bounce clips together (or in the case of X3, Flatten Comp) where necessary seems like a minor inconvenience.
 
Personally, when I do sound-on-sound MIDI takes I like to have the option to manage the layers/lanes separately, and would probably never enable a merge option if it existed.
 
The only thing I'd really like to see in this regard is a little more consistency/flexibility in how clips are merged visually in the parent track whether lanes are showing or not

Hi there,
I guess it's down to habit really. Ever since I started with Cubase on the Atari around 1989 I've been used to auto merge when doing overdub midi recording. But I guess you're right that using the "Flatten Comp" is pretty quick to use. Maybe I need to spend more time getting used to using layers/lanes. Thanks for you input it's appreciated

One thing that would be nice was if when recording say a 4 bar loop that each take was rounded off to the full 4 bars.
is there a reason behind that? Here's how it looks when I do it.
 

 
 
 

In SONAR conventional MIDI clip boundaries are defined by the start of the first event, and the end of the last one. If you convert the clip to a Groove Clip (right-click or Ctrl+L for Groove Clip [L]ooping), SONAR will pad it with empty space to start and end on measure/beat boundaries. If it doesn't fill the measure as expected,  you may have to correct SONAR's estimate for Beats in Clip in the Groove Clip section of Clip properties in the Track Inspector

Hey Adralicus, these are the 2 things that bothered me in the Sonar software for a while as well, as all the other DAWS i use have that function.
As everyone has said here it just works different, its not a show stopper but just odd, I use logic 9 and X,
Reaper, Pro tools, and they all behave the same ( you can over dub w input quantize on and it loops w out beats dropping out w each pass, and also the end of the loop issue where you have to drag the end of the clip to the end of the measure to make it a full bar) Its weird behavior but i think thats how it is w sonar.
If i recall i think one version of X1 (not sure what update a,b,c,d it was)  the input quantize actually worked like it should w out parts dropping out, Im pretty sure it was one of the X1s the when i added an update it stopped working,
Anyway i hear you on that it would be a nice option if both these things worked how we would like them.
Tommy

I hope the next version includes the option to auto merge midi when loop recording:)