Definitely not alone. Still an intermittent problem, although it seems better in the last few versions. I had it a lot more during X2 I feel. Pretty annoying since there doesn't seem to be anything that reliably reproduces it. Only thing that fixes it is restarting Sonar. Pretty embarrassing when you're there with a client.

Me too. 
I thought I had executed some elaborate procedure to get in to this state, but it seems I'm not alone!
As far as I recall it's only happened since Cambridge (to me, anyway), I think
 
jdf

I've never had any problem splitting clips. Maybe I'm not beating it hard enough.

I have seen this issue as well. Only a restart of Sonar would fix it.

My problem with the X3 split function is it cuts the visible track (i'm trying to cut a 2 hour show into individual songs) and seems to save the song ok ( splits before and after the song i'm editing), I've deleted the sections before and after the song i'm working on, the problem seems to be with the audio in the audio folder, as this is still the same length as the original 2 hour show ( if i play the wave files outside of X3 on a media player everything is still there!!), previously all the wav files were cut to the song i'm working on... Help!

The same thing happened to me this morning.  I was going through the vocal clips I recorded yesterday.  I was splitting four or five clips at a time by lassoing them and using 'Alt+Click' on the selection.  The clips on the screen did not split.  When I looked at the Edit menu however, 'Undo Split Clip' was an option.  I closed Sonar and restarted.  After that splitting clips worked as usual.
 
Note:  After repeating this on three vocal tracks and using Melodyne for some pitch corrections, nearly all of the clips on one of those three vocal tracks had fades on them.  I haven't seen that happen before, but the the Smart Tool gave me the Crossfade Icon a few times, so maybe it was operator error.  I don't know.

Lauriefin
My problem with the X3 split function is it cuts the visible track (i'm trying to cut a 2 hour show into individual songs) and seems to save the song ok ( splits before and after the song i'm editing), I've deleted the sections before and after the song i'm working on, the problem seems to be with the audio in the audio folder, as this is still the same length as the original 2 hour show ( if i play the wave files outside of X3 on a media player everything is still there!!), previously all the wav files were cut to the song i'm working on... Help!

This is unrelated to the problem being discussed.
 
If i were you, after splitting each song out into it's own clip, right click it and select "Apply Trimming"
When you've done them all, do a "Save As" to a new location and ensure "Copy Audio With Project" is checked.

Thanks Bristol, that seems to have cured the problem :

Just to say I had the same problem, tried all the fixes listed above and found rebooting Sonar (X3 Prod) was the only thing that fixed it. Thanks for the advice in this thread.