This may not be the issue in your case, but when I run into this problem I now double check to make sure the SONAR main window has focus. Often, if I'm in some other window like a synth or a reverb and I try to start or stop playback with the spacebar, nothing happens because the main SONAR window doesn't have current focus, it can't see the spacebar keypress. If I then e.g., mouse click on the SONAR Play or Stop buttons, that works since doing that simultaneously claims focus on the window and performs the start/stop action. Having done that, a subsequent spacebar would then operate the transport as expected since the main SONAR window is now in focus.
If I reach for the MCU transport controls when the spacebar doesn't work, the MCU start/stop command works but I'll still have the problem of subsequent spacebar transport starts/stops not working since the MCU transport action doesn't change the GUI-keyboard/mouse focus.
Obviously, other VSTs/DLLs need the keyboard/mouse for their own functions but for me it's easy to forget that the display is not all SONAR all the time.
If this is not relevant or helpful, please just ignore me... Good luck.