I have a setup of a RPI3, latest OSMC and a string of 94 WS2801 LEDs. I had this setup working a while back on an old version of Hyperion (and before that Boblight) on an RPI2 (openELEC) so I assume the hardware is OK, (I've also checked continuity with a multimeter).
The first 50 LEDs (at the start of the string) work exactly as expected and I can control them fully, none of the LEDs after that will light up at all. I've tried changing the baud rate, grabber and "outputs" in the HyperCon software, but no joy.
I have a feeling that the number 50 is not simply a coincidence, and also that if I dim the luminance gain, no further LEDs work, the same if some LEDs are off due to the backlight setting, it still does not light up after the 50th LED.
The PSU i'm using is a DC 5v 10amp unit, albeit a cheap ebay job it has been reliable in the past (running both the LEDs and PI). I do wonder if the increased draw from the PI3 is causing an issue (I also see the power symbol during playback on the top right of the screen). As I understand it each LED draws 50mA (x94 = 4.7a + 2.5a for the RPI = 7.2 amp draw total).
I can upload the logs & config later if need be.