Interesting, I'm going to have to grab a set of these and do some playing. A have a set of 3-wire strings that use the CYT3005 chip. The intention was to figure out the protocol and incorporate it into my pixel controller, but I haven't made much headway in reverse engineering the protocol. Are you looking at this with a logic analyzer? It could be some other chip and there's no reason that 3-wire has to use Manchester encoding, itr could just as easily be a simple asynchronous data format. Looking at the data going into the last pixel may be more helpful. You should see some amount of data followed by the data that you are seeing now. Whatever data bits precede the last 27 pulses are the bits that are being grabbed by the last pixel.
The bit sequence you see coming out of the last pixel might be what tells each pixel that the data frame has ended and they should output their data bits to their leds. Do the bit values change or are they always the same sequence?