I had Guru 1.6.12 installed and in song after song that I loaded in Sonar 8 PE only Guru would play and occassionally one or two other soft-synths, but ones like Vanguard and Rapture would never play. I could get Vabguard and Rapture to play if I loaded up a new instance on a new track, but the ones that were already there - although showing as receiving midi data - would never make a sound.
I reverted back to 1.5 and problem solved. All the original VSTi's (with their respective midi data) played fine.
At a guess I'd say it's because of the extra outputs in 1.6.x, which has 16 stereo outputs instead of the 8 found in 1.5.x. Sonar must be having trouble allocating the unexpected outputs when it reloads a song made with 1.5.x.