This just in from Yamaha..an explanation of the sync problem that I was having with a CS6R. It would seem that in Yamaha's eyes it's a feature. Be warned that in my eyes it's not a feature to anyone who plays in real time which I believe would be about 98% of us. Your milage may vary.
As product manager for Digital Musical Instruments here at Yamaha, I am very concerned with issues like you mention. There has been considerable confusion in regard to the arpeggiator synchronizing function of our most recent line of synthesizers. I have performed extensive testing of the arpeggiators sync capability and can assure you that it does synchronize with external MIDI clock. I hope the following information will adequately explain how you can achieve the results you desire.
Because there are several categories (types) of arpeggiator patterns intended for different musical purposes (guitar strums, drum patterns etc.), the triggering implementation (both internal and through MIDI) is a little different from previous instruments. But it does synchronize perfectly with external MIDI clock messages recieved by the MIDI in of the CS6x(R), S80 and S30.
The reason that it doesn't seem to sync properly is that the actual arpeggio pattern is offset (delayed) by a 32nd note (independant of tempo as it must be, to be in sync). This is a predictable musical value that represents a "window" of opportunity that the arpeggiator gives you in order to determine how many and which notes you wish to arpeggiate.
When you are aware of this 32nd note offset, it is possible to trigger manually (by anticipation of a 32nd note) to achieve the desired result, and through MIDI by offsetting the arp trigger note[s] by a 32nd note.
When these methods are used it is possible to achieve perfect synchronization with any and all arpeggiator patterns in the CS6x(R), S80 and S30.
Thank you for your support of Yamaha synthesizers and if I can be of further assistance feel free to contact me.
Digital Musical Instruments
Yamaha Corporation of America