Very intermittently, when i press the right turn signal, the left one will flash also, out of phase, but like hazzard light. This only happens to the right turn signal, and is very intermittent. Is the relay likely to be the main suspect? I have cleaned the turn switch internals previously, but it happened again recently, and I'd love to track it down!!

Turn signal weirdness if often a symptom of dirty starter brushes.

Wouldn't that cause the symptoms to manifest at both turn signals?

I've had the dirty starter brush syndrome, I had funky indicators and headlight and starter failure to spin. Tried the backspin method a few times, it did allow me to start but the symptoms came back immediately. I abandoned my ride came home and cleaned the starter. The starter is a tight fit into the engine it is a good idea to put a smear of Copper Kote on the mating surfaces, it will help in removal the next time around. The job itself should take about an hour.
Regards Martin.

@BooG wrote:This only happens to the right turn signal, and is very intermittent. Is the relay likely to be the main suspect?

Describe very intermittently. Once a month, one a day, once every few right turns?

Pull the flasher relay. Assess its condition for damage and clean all its contacts. That is simple and will fill time until the next event when you can work on the starter. 

Intermittent problems are troublesome to track.

The indicator relay has 2 power sources one switched and the other not. If either is missing strange things happen. Check the starter brushes as one power supply comes via the load shed relay and also check fuse #7 as that is where the second power supply comes from. Good tip is to replace the fuse/s because those blade fuses do suffer from age just like K riders. Don't just visually check the fuses use a meter to check for continuity as corrosion inside the plastic body of the fuse will cause an open circuit and it wont be visible.

Another interesting symptom to muse over....
so when I am standing still with the engine running, the right signal flashes as it should. If I rev the engine, it goes into the "out of phase hazard flashing" thing, and then returns to normal once the engine settles to idle again...??!
Sporadic can sometimes mean anything from daily, to once every year...no apparent pattern or logic to as or when. Currently, it seems to be occurring every day, so i guess that counts as permanent right now. 

Hey BooG, did you get this sorted?

Mine's doing the exact same thing. Left indicator flashes normally at idle, but both (left and right) flash when engine revved. Four-way flasher operates normally. Right indicator is also operating normally.

I'll clean the starter to see what happens.

Typically, it's behaving at the moment....!!!
However, I just received the new brushes and seals for the starter, so I'll rebuild and clean it when I get a mo and report back.
Let us know how you get on!

My left indicator came on and stayed on even after removing the key, bike run as normal but had to disconnect the battery to turn it off, starter motor brushes bought from local auto electrician all fixed,

While we're talking stoopid behaviour: over-temp light coming on with high beam after around five miles. Turned out to be a shitty connection on the battery earth strap. That meant that LFB had been relying on a 200mm length of 11 amp wire when starting (shudders). No fire but definate signs of meltdown.

Hi Dai, you should have seen the elect mess on the LT I just aquired, one key fits all 7 or 8 locks but does nothing in the ignition but turn, seperate rocker switch that's live all the time, wires from the ignition cut/Brocken, after market alarm fitted with speaker wire, and they were fused but melted together before the fuse, on/off headlight switch added with same wire, all sorted now but each time I connected the battery I had my fire extinguisher ready, it runs on all four now, 2 blocked injectors I dead spark plug and 2 dead leads, and replaced the licorice hoses and ............. 

Gary could please post the local source of your starter brushes.
Regards Martin.

I thought hard (for all of about six seconds) on how to stop LFB from using the in-loom earth wires as a starter return in future. Answer: isolate the entire wiring loom from the frame and have just one 32 amp earth from the loom to the battery. Next time it decides to grow fur under the earth strap it just won't turn over.

Fire hazard - eliminated.

Hey Martin, took the used brushes to Redcliffe auto electrics on Anzac ave, they made a set cost me about $25, that was years ago so they must be doing it right, they are still there, cheers

Thanks Gary I thought you might have found a local manufactured set. However still good to know that they will do this for you. I did find these a while ago which should fit with minor modifications. http://www.ebay.com.au/itm/Starter-Motor-Brushes-2-Nippon-Denso-For-Yamaha-XJ-650-L-Turbo-Seca-1984-/352068070004?
Regards Martin

Well it ain't the starter. I swapped out the starter for a refurbished one I had, but nope, the problem still persists.

I'll have a look at the wiring diagrams (I'm trying to sound knowledgib knolegi smart here) just for the hell of it.

My best guess is the indicator relay.

possible connector issue to the flasher relay Blakey ?

those connections  sometimes hide a bit of corrosion in the socket part of the spade ... but also pop the cover off the relay and look for cracks on the soldered connections to the pc board from the connectors ..

worth a look any how

Put a new fuse in #7 doesn't matter if it's blown or not just replace it. No guarantee but a good bet.

Have just completed the starter rebuild....new brushes and a clean up as per instruction on forum....took it for a test ride and it seems to have done the trick! No probs with the signals, and the engine was very eager to start up! I'll keep an eye on it all, because it was an intermittent problem, but early signs look good. Whole job from removal to test ride only took about an hour. The battery I'm using allowed me to withdraw the starter without removing the tray etc, so that helped some. Hardest thing was setting the brushes in the springs when repositioning the commutator...a little fiddly, but managed it.
Thanks for all the pointers from members....always plenty of wisdom on offer! 

Good result, did you smear a bit of Kopper Kote around the housing. A mates starter corroded itself in and he had to attach a home made slide hammer to remove it.
Regards Martin.

No I didn't! A smear of oil was all I put on. I may well go back in and do that seeing as its so easy to remove.

Guess what??? Same issue again today! Looks like the starter brushes didn't solve it, so into the relay next!! 

Working fine again now....didn't do anything. Its great, innit.....still puzzles the sh@@@++t out of me though!