Johnny, I would gladly stop using the software if there was an alternative. There are none (trust me on this one!)
Software is vArranger. I used Software A and Software B, not to confuse people. I have tried two different ASIO cards playing with buffers etc. Internal WASAPI.. can not avoid it. It is internal to to software.... no "clock" sync.  It spits WAV files that have exponential latency. Drives me absolutely nuts. 

This is a problem that its possible to solve using audiosnap. You would have to extract a tempo map from the original tracks (choose a track that best defines the tempo like a percussive track) and then fit the other clips to match this tempo map.
This topic might shed some light on how to do it.
 

I do this often with several different versions of a song. Several ways to do this. I personally like to map tempos by hand. So I map the tempo of each of the songs Saved As various tempo map names. song 1 tempo map song 2 tempo map song 3 tempo map. Then i'll Apply the tempo map i like to All of the Audio clips by copying the tempo map from the tempo list of one to the other. Unifying the tempos of all the clips. Once each Clip has been Mapped, they are perfectly controllable via Audio Snap and the tempo map. Very fun!

Thank you Noel!
Thank you Blogospherianman!
 
Tempo map looks like an interesting power tool. I have tried it, but still, tracks have issues.
I will play around with it more in the next few days. In the past, I was able to happily avoid using tempo corrective tools, but this time I might just have to dig in it.
 
I am still hoping / trying to press on developer to sync software to correct clock, so the outputted files have correct tempo maps... 
As I understand, standard approach is adhere to sound card clock?
 
Thank you.

Hi fellows.
Sorry to revive this post...
I was trying to fix my track in Cakewalk using Audiosnap, I was able to partially make it workable.
The problem is, that I am very new at this approach (fixing tempo in audio clips) and confused by process.
 
What I mean is, that I do not even know if it is Tempo mismatch or latency issue.  Initially I though it was latency, so I tried many things common things, like not running extra stuff on background, raising/decreasing buffers, external ASIO interface... and many other things to record these tracks. The program that I am using is not a VST and it does all "recording" internally, so I can only import WAV files to Cakewalk...
 
Long story short,  looking at the file, I can not figure why it is out if "out of sync".. Is it  audio latency that is exponential or tempo map problems caused my MIDI clock of that program.
 
I was wondering if anybody here, who knows about those things, can help me and take a look at actual audio file and tell what is wrong with it... I would appreciate it very much.
 
P.S. If this was a single instance of the problem, I would find one way or another to "fix it", but I have many arrangements that share same problem and I just want to find a solid "common" approach to fix these. But before even starting to look for the cure, I want to know the cause. If it is Tempo Map problem, Latency or both... or something else.
 
 
Thank you,
Mike.
 
 
 

PM me a link if ya want and I'll check it out.

If you need further info on Groove Clips/Extracting tempo or AudioSnap, here's some resources...
 
Tempo Maps



 
AudioSnap



 
GrooveClips / Working with Tempo

bluebeat1313
What I mean is, that I do not even know if it is Tempo mismatch or latency issue.  Initially I though it was latency, so I tried many things common things, like not running extra stuff on background, raising/decreasing buffers, external ASIO interface... and many other things to record these tracks

You have not really described your signal path and devices in any detail, but I find it hard to conceive of how audio latency would be "exponential." The most common cause of the problem I think you describe is that you have recorded one set of tracks at one tempo and another set of tracks at no regular tempo whatsoever, but the basic phenomenon of increasing displacement is an effect of tempo mismatch.
 
Assume for the sake of demonstration that you have recorded to a regular metronome on both track set 1 and track set 2 but they are set at a different metronome frequency. If you align the first beat of the two sets, then the faster metronome will result in a track in which the equivalent note/beat falls ahead of the slower metronome  track from the second note onward, and the difference will get progressively more marked as the tracks progress over time. A graphical representation of this phenomenon using letters as notes and dots as time between notes is:
a...b...c...d...e...f...g...h...i...j...k...l...m...n...o                           faster metronome
a....b....c....d....e....f....g....h....i....j....k....l....m....n....o            slower metronome
That is the expected behavior if the tracks are recorded at the correct rate for each metronome and has nothing to do with audio latency. It will occur whenever the tracks are at different tempos, and the displacement from alignment will increase over time.

Couldn't you just slip-stretch the end of the clips that are longer to match the end of the clips that are shorter? That would solve the problem if there was a slight tempo mismatch.

Oh wow, I forgot that this is a serious forum.
I checked the post for two days, than closed the window, thinking it will not get attention. For some reasons I do not receive email notifications when reply is posted.  Silly me. As developer of the software explained,  his program does not adhire to specific clock. The tempo set to record these Wav files is correct... he said latency caused by jitter and by design, as software is used mostly for "live" performing and so that midi parts would play smoother when triggered in live scenario... Well, explanations...
 
I was very persistant and developer confirmed that he is working on Clock Sync In option. As I understood, it will solve my latency problems. Instead of bugging you guys, I think it is wise for me  to give developer a chance to fix this, while he is in the mood for it  ;)
 
P.S. I think I had issues with  Audiosnap because latency was not consistent. 
 
Thank you!