I mix and master all-in-one, and with the exception of a few rare occasions I NEVER have this problem.
 
I right click, hold, and drag across all clips I want to export. This selects those clips. Then I export, and Sonar does just what it should...it exports just those clips.
 
The aforementioned rare occasions occur when I forget to select the clips, which is almost never these days.
 
Also, for reverb tails I clone a track and use it as a dummy. I lower the track's gain all the way, then mute and archive it so I'm certain it won't sound, then position the clip so it ends where the reverb tail should end. Then I make sure to include it in my selection.
 
 

SorcererXIII
I know I can work around this by manually selecting what to export with the mouse, but I am lazy. 

I never understood this, you put hours of work in to a project but get lazy with setting in/out points ?
its a whole 6 clicks.

Hangdog Cat 
Also, for reverb tails I clone a track and use it as a dummy. I lower the track's gain all the way, then mute and archive it so I'm certain it won't sound, then position the clip so it ends where the reverb tail should end. Then I make sure to include it in my selection.

That's far too long winded for me.
 
I simply slip edit ANY track out to the point where I'm sure the reverb has stopped sounding as use that as my End Marker

 

Bristol_Jonesey
That's far too long winded for me.
 
I simply slip edit ANY track out to the point where I'm sure the reverb has stopped sounding as use that as my End Marker

 
I'll try that next time. But I guess I'm paranoid about unwanted audio creeping in.
 
Thanks,
The Long Winded Hangdog Cat

Cakewalk has to offer the opportunity to end a project at any point an user wants.

Hangdog Cat
 

Bristol_Jonesey
That's far too long winded for me.
 
I simply slip edit ANY track out to the point where I'm sure the reverb has stopped sounding as use that as my End Marker

 
I'll try that next time. But I guess I'm paranoid about unwanted audio creeping in.
 
Thanks,
The Long Winded Hangdog Cat

Do it on a Midi clip. No audio to creep in 

chuckebaby
 
I never understood this, you put hours of work in to a project but get lazy with setting in/out points ?
its a whole 6 clicks.

I use "select all" for more than just exporting.
 
But usually even after everything is written I spend an hour or two doing nothing but make a minor change (that usually requires deselecting), export,  listen to it in the game or in itunes to make sure it sounds good with gameplay or in a playlist with other music, etc, then change again.  Also since my music has to continually loop and the mouse selection won't work when you mouse over the yellow loop points, I need to disable the loop, then click, then re-enable the loop, or else send an end marker (which will have to change if I lengthen the piece) and click on that then do the select from=start, thru=end.  So I end up doing this over and over.
 

 

BassRocket
I got my not working Stop at End of Project function to work by using the putting the Now Time marker at the end of the song and then using the select module in the Console and clicking "Set From Now" that (should) mark all the measures from the Now Time till the actual end of the song.
Then make sure all the Tracks are selected top to bottom and hit Delete. Hope it works for you.

I did this also, but it didn't help.  That's why I tried deleting all of the tracks and buses in the project until it was just an empty project.  So there is a hidden not-in-track, not-in-bus, non-tempo change event that Sonar saved into this particular file at measure 95.  I can add a single track and make it longer than 95 measures by adding a note or something past it, but it will not allow the song to be shorter than 95 measures.

I just had another project that this happened to (i.e. deleting all tracks, events, tempo changes, etc. still does not affect project end).
 
There is a couple of things I did in this project I didn't do in others.  I had to copy an instrument track from another project so I saved out a track template from the other project and loaded it into this one.  Then copying and pasting the automation wouldn't work unless I split the instrument track and copied the midi track and synth track separately.  But when I re-assembled using Make Instrument track, that automation would disappear from view but still affect the synth.  Another user explained that unless the "Synth Automation Track" dropdown in the synth rack is set to the MIDI track, any automation on the synth will disappear, never to be accessed again.
 
Although I did do this step, I wonder if there isn't more data that disappears whenever you split/make and instrument track.  Perhaps these automation lanes get saved, hidden, remaining even after the track and synths are all deleted.

I had a project that was supposed to be around a 20 or 25 minute track, and for some reason it ended up being several hours long. (I posted about it here somewhere. I should find it & see if I ever posted what I ultimately found.) The client had asked me to import a sound effects clip, which he provided. While the clip appeared to be just a few seconds long in this project, it turns out it was some kind of loop, with some hidden coding that Sonar could see. This coding forced the project to be about 3 hours long, iirc. I had trimmed the clip, but that hidden coding still hosed the project up. Eventually I went in and just rendered (bounced to clip) every single sound effect he had provided me, and that solved the issue. I may have had to go in & find some sort of event marker & move or delete it or something, I don't recall.
 
My point is that there is most likely some kind of user action which leads to the "too long" or "too short" issues. Sometimes it is a PITA to find the cause, though, no doubt.