Make sure all your tracks are visible, including any archived material (hit shift + h)

Also check there are no Tempo Changes or Mater/Key changes out past where you think the end should be.

Well, there's no meter/key changes, clips/tracks are not locked, I used no automation, there's no MIDI events past bar 98 in any track (long fade to bar 104). I'm just puzzled.

Still trying to figure this out. I have 2 audio tracks that'll let me drag the ends of the clips, but there's several MIDI tracks that seem to have no end to grab hold of so I can drag them. Even though Sonar thinks the end of the song is out at bar 174, the track view displays bars way out past 174 with no end of clips.

Can you try putting a split on those tracks then delete the ends?

Yes. That finally did it. Thanks. I tried that before and it didn't work. Even this time, the little scissors thingy showed up real good for the audio tracks, but was real hard to activate on the MIDI tracks. Then, it was real hard to see if I was selecting anything for the delete. I thought maybe the problem was me getting used to things looking a little different in X2, but I also went back and reloaded X1 and still couldn't figure it out. Well, it's done now, but I don't understand what was going on.

Sonar gremlins. They're little buggers. ;-)

Glad it worked out in the end. Cheers.

Oh and in the future if the Split Tool (scissors) are giving you a hard time try setting the Now Time to where you want the split, select the clips to be split then press S on the keyboard. I've had trouble with the Split Tool in the past and that process ends up working without fail. Also there is another bug that sometimes selects tracks all willy nilly and you end up splitting tracks that you don't want to. I solve that by locking all the clips of the tracks I do not want to be effected. Cheers.

I had the same problem yesterday. I copied and pasted part of a MIDI track and suddenly I had a bunch of extra blank measures at the end of the song. Highlighting the MIDI track and selecting "Bounce To Clips" fixed it.

I've just joined this forum because I have exactly the same situation and you good people are all clearly extraordinarily bright.  

My project ends at bar 27, but Sonar X2 keeps going until bar 93.  I tried everything advised here and more before I resorted to the internet search that led me to you.  There is nothing, nada, zero, zip beyond bar 27.  I've done a split at bar 27, selected everything -- all 22 tracks -- from 27 through 93.  But Sonar won't let me cut anything -- the cut option on the menu is grayed out.  Because there's nothing there.  OK, so what, you might reasonably say.  Minor inconvenience.  Au contraire.  Because I export my Cakewalk (excuse me, I mean Pro Audio, no, I mean Sonar -- I've been using Cakewalk/Pro Audio/Sonar since it was nothing but MIDI in a DOS version -- but I digress).  

Anyway, I export my Sonar files in XML, which I then import into Finale to distribute scores to singers.  Here's where it gets nasty.  Finale imports all 93 measures from the XML file Finale.  And Finale also says there's nothing there, and it won't let me delete those measures.  The "delete measures" option is grayed out, just as in Sonar.  Finale, like Sonar, doesn't think those measures exist.  

(Now maybe there's some hidden factor lurking.  This 27 bars is saved from an earlier project originally created in a much earlier version of Cakewalk.  But that earlier project is 120 bars, not 93 bars)  

Halfway through writing this, I finally had the brainstorm to resolve it by copying just those 27 bars to a brand new, virgin file.  And that fixed it.  But I had to go into each track and individually set it to a new softsynth I had to re-create in the new file.  Now that truly is a minor inconvenience which may render this whole problem too trivial to trouble you good people.  

But I've got other files like this one, and besides that, I'd like to understand what's going on.  

Anyway, thanks for any insight you can give me, or, failing that, for letting me vent about the six hours I've just spent trying to figure this out.