FWIW, I too am having issues with the sustain pedal not working with an Alesis Q88 in Rapture Session. It works fine in Dimension Pro. Rapture completely ignores it. The issue is also in the other sections of Rapture as well.
 
Not a big deal as I rarely use Rapture but if Sonar is going solely to Rapture then it needs to be fixed.

 
Finally i found the solution to my sustain problem. I really had to change midi channel before this problem resolved. 
 
First i have to change custom to all that i can see midi channel box. There was 'None' selected. I change it to channel 1 and now everything work as it should be with my Roland BK-5 keyboard. Thank you all for your help. I appreciate it.
 
 Edit: Red box is little bit wrong place. Sorry. Midi Channel box is one before it. There is letter c. B is midi bank.
 
 

WOW - thanks so much for your post.  I have no idea how my settings changed but this is exactly what happened to me too.  Marked the box and my sustain pedal is back up and working.   Thx.

Sorry for the somewhat necropost here.
I'm new to Sonar, where did you go to change the midi channel?

Here is picture where to go. Hope it work. In blue box you must change it 'All'. And In little red box you change channel '1'.
 

odyssey70
Here is picture where to go. Hope it work. In blue box you must change it 'All'. And In little red box you change channel '1'.
 

It did work!! You rock man, thank you so much!!

Great, i'm glad it's working now :)