Is there a way to "sync" 2 sets of wav files?

You can convert the waves from software B into groove clips within Cakewalk and then stretch them to fit with the other wave files.

bluebeat1313
mritenburg, thank you for suggestion, however this seems a very tedious approach.  Latency starts to happen at around after 20 seconds into the tune and increases exponentially.  I thought there would be a way to automate this process because all 5 tracks are synced to each other...
 
Can anybody else please comment.
 
Thank you.

You're saying 2 clicks to enable groove-clips is tedious?  
 
Well, you can try Audio Snap, but it's actually more work.
 
 

The problem you describe is that one set of tracks is not synched to any standard clock/tempo. Simply stretching the whole track will not eliminate the variability. If you create single groove clips, or any other method of stretching, from those full tracks, the altered tracks will remain synched to the others in their set, but the tempo for the whole set will likely wander relative to the other set. You might be able to sort of automate the regulation of that wandering with a tempo map, audiosnap or melodyne, but you may end up having to split the tracks into multiple clips and stretch individual clips. This could be tedious indeed. 

I've not tried this,  just trying to think outside the box...
 
So say you take just one track, extract a tempo map/make a groove clip , then save that project as "tempo map"
 
Then save the project as "track1".
 
Then, set the tempo to some average so that everything is the same tempo (e.g. if the tempo range in the map was between 115 and 125, you'd set the tempo for the whole clip to 120).
 
Then save the groove clip as "clip1".
 
Now start a new project, "track2" with the second wav file, extract a tempo map/make a groove clip, set the tempo to the same as clip1 and save the clip as "clip2"
 
Do the same for the other three tracks.
 
Then open the original "tempo map" project and drag each of the saved clips into the project as new tracks.
 
So basically you're:
 
1. Getting a map of the tempo for the song from one of the tracks.
2. Evening out the tempo of all the tracks to a fixed tempo, saving each track as a groove clip
3. Importing them into the original project, so that the original song tempo map (with all its variations) is applied evenly to all tracks.
 
There's probably some work involved in setting the fixing the time-markers when creating the groove clip, but wouldn't something like this work? 

Personally I would avoid Software B. What sort of DAW does not export a proper wave file?? I'm curious. It's allowed to use names here too :)  

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.

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

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.

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!