Tracks Being Shifted

(I am using X3c producer)  I have a project which consists of three songs which are being recorded within the same project, one right after the other.  A week ago, I did some recording of the third song and playing the three songs (what has been done on them) worked just fine.  Due to other obligations, I had not done anything since today.  I opened the project, scrolled to the third song and it was working fine.  I returned to the beginning of the project (where the first song begins), which starts out with two acoustic guitar tracks (for the introduction).  The vocals lines began way before the introduction began. What!?!?!?  Well, it seems that the vocal tracks got shifted to the left.
 
When I had previously worked on the project, I cut out the dead space and some of the breath sounds in the vocal tracks which gave me pieces of tracks (or clips) spread through the track.  This isn't a problem because the clips aren't moved and the vocals are in the appropriate spots.  However, when the tracks got shifted to the left, I believe the spacing between the clips was also reduced.  Consequently, I've got to either 1) shift each clip to where they are supposed to be (which is more difficult than it should be because the songs were not done with a click or set metronome due to the many subtle fluctuations in the the tempo throughout.)  or 2, re-record the vocals.
 
My first question is, has this ever happened to anyone else?  Then, what could have caused this issue?  Is there some sort of setting which caused this?  Is this a quirk in the software which needs to be rectified?  
 
This did happen before (I believe I was using X2 when it happened but it could have been X3) but this was a simple fix because the two tracks that got shifted were not broken apart so dragging them to their correct spot was easy.  
 
Insight on this issue would be extremely helpful.  I have already spent a couple of hours on trying to figure out where clips go and moving them and I still have a ways to go.
 
Thanks in advance.

Hmmm.  That makes sense.  On the third song, I did change the tempo and it was recorded with a click track.  However, I shifted a bunch of clips around already so I might mess things up if I change it back to 120.  Grrrrr.  

"would making the tempo change in the timing map where a follow-on song starts make a difference?"
YES
You want to "insert" a tempo change where the new song starts.
I frequently have subtle timing changes in a piece, BUT you have to program all that before you record the audio.
Tom
 

I'm not Tom, but, tempo and key/signature are in the Project pulldown menu.
 

You're welcome!