My first problem since upgrading to Sonar Platinum after finally moving on from X1 Producer...when I highlight the separate clips in a track and click "Bounce to Clips", they still just remain as separate clips. I'm doing it the exact same way I used to do it in X1 and it just won't make them bounce together.
 
My second problem is that I was just recording something that has an mellow intro that transitions into a huge sounding A part, the transition sounds so strong in Sonar, but then when I export it to a WAV, that A part ends up sounding LOWER than the mellow intro. You can understand how that would defeat the purpose of trying to make that transition sound huge. Any advice on this would be appreciated. 

joeyfreeze
My first problem since upgrading to Sonar Platinum after finally moving on from X1 Producer...when I highlight the separate clips in a track and click "Bounce to Clips", they still just remain as separate clips. I'm doing it the exact same way I used to do it in X1 and it just won't make them bounce together.

 
I can't duplicate, can you post a screen shot (use imgur.com or the equivalent) that shows the track and clips?
 

My second problem is that I was just recording something that has an mellow intro that transitions into a huge sounding A part, the transition sounds so strong in Sonar, but then when I export it to a WAV, that A part ends up sounding LOWER than the mellow intro. You can understand how that would defeat the purpose of trying to make that transition sound huge. Any advice on this would be appreciated. 

 
Another head-scratcher. Can you see a difference in the waveform? Are you using any plug-ins? Stray automation?
 

Here's a Youtube clip a made showing the bouncing process not working...
 
NEVERMIND...wouldn't let me post a Youtube clip...
 
As far as the dynamics...upon looking at the wave form of the WAV file, it looks significantly bigger when it reaches that A part, but certainly doesn't sound significantly bigger like it does in Sonar. Kinda depressing. I do have effects like reverb, compression and EQ on lots of the separate tracks, but that's pretty much it. Nothing crazy. 

You do not have enough posts and the account is too new to add links. When inserting images using imgur make sure to add the link to the image (the url will have an image extension) and not page (the url without a file extension) like this:

Oh, I thought I did it that way! Well, thanks for posting it anyway, at least now it can be seen!

The broken image I saw when posting was https://imgur.com/VZIUVse which is a page containing the image. I made the embedding image above by adding an image extension to the url. Although I probably used the wrong extension (.png) imgur resolved to the correct file.
 

Thanks for the GIF, that's definitely unexpected behavior so let's do some diagnostics.
 
It looks like the track is frozen. Normally if you have two clips in a track and then freeze, they will appear to bounce together but the clips remain separate so that you can return to the unfrozen state. I rarely use freeze, but what happens if you unfreeze, and then either re-freeze or try to bounce the unfrozen clips?
 
Also, what happens if you bounce each clip to itself, and then try to bounce the two together?
 
As to the dynamics issue, I assume you're exporting to a stereo mixed WAV file. If you create a new SONAR project and import that WAV, a) does the waveform look correct, and b) does it sound correct? If not, what does it sound like if you open it in a Windows playback option, like GrooveMusic?
 
Finally...what kind of audio interface are you using? If you're using the computer's internal audio, Windows might have some default "enhancements" that are intended to create consistent levels in a playlist or alter EQ. I've been trapped by this multiple times when creating audio on my desktop machine, bringing it into someone's laptop for playback, and then having it sound horrifying.

Those look like FX clips (a clip FX) try bouncing them down separately first (Like Craig said).
Which FX are you using ?
Rather than drag/select, Try holding the right mouse button down and drag (rubber band/lasso) around the 2 selections then choose bounce to clips.
 
Something else to consider is "Linked clips" or "Locked clips" though im not sure if that would prevent a BTC
 

Anderton - Thank you for suggesting that I import the exported WAV into Sonar, because the dynamics sound perfect in there, so it must be something that Windows is doing. Just hope it doesn't end up that way on Soundcloud or whatever...
 
I tried bouncing the clips to themselves, and it seems like they won't do that either. They remain as FX clips no matter how many times I bounce them to themselves. Unfreezing and refreezing would probably help more if I hadn't split and pasted the clips around AFTER freezing. "Bounce to tracks" after I've highlighted the clips seems to do what I want, but it creates an extra track in the process, which is kinda inconvenient, but all I need to do is delete the previous track I suppose.
 
chuckebaby - That lasso tool didn't help me bounce the clips either. On those two clips, the effects are Sonitus Reverb and Sonitus Wahwah.

Its easy to press K by mistake (thus locking the clips).
I would double check to make sure they are not linked or locked.
I misunderstood your last comment but if they are Frozen clips, unfreeze them before trying to make edits.
 
Freezing a track is done to free up resources/not to edit. If you want to use that frozen data to edit, Drag it to a new empty audio track.