I'm a bit embarrassed to ask this question but here goes:
If I increase the rpm to about 2000 or so there is a real clatter, almost like I'm lugging it. Above 2200 rpm or so it's a bit quieter.
It seems illogical to me that I can pull away away at 1500 rpm without any noise, yet 2000 rpm sounds like a bucket of bolts being rattled.
Did you ever get to the bottom of this David ?
I just revisited the thread and noticed that yours is a 2005 model. I have owned 2 St1300s, both from new. A 2006 A6 and a 2013 A9.
The A6 always used to pink badly when under load, and when hot. After prolonged uphill rides the engine just felt weird - can't describe it, but the few times it happened i decided it was time to let it cool down. I had it checked out. Normal apparently.
Most of the time it would purr along quite happily, but it did not have the low down pulling power that I enjoyed on either of my previous ST1100s. Tight uphill hairpins would require a lot of clutch control. If I didn't keep the revs up it would clatter away and sounded as though it was about to stall.
I tried a few things which helped. Quality Fully synthetic oil seemd to be better, and if i was heading onto the continent, i would use slightly thicker grade 10w-40 rather than 10w-30 ( have ingot that the right way round ?) .
I also noticed that higher octane fuel helped a lot. Here in the uk we typically have 95 and 98 RON. Using 98 helped a lot. The label on the tank gave the impression that 95 was just about Ok, but when I compared it with the label on a Usa model, and did the conversion our 95 RON would not have been in the acceptable range!
The 1300 is able to take E10 fuel. 10% ethanol. Its hard to avoid in Europe, but is not common in the Uk. But that was horrible. As if someone had fixed a set of wind chimes to the bike. And setting off would be the worse.
And a trick my police instructor gave me. "Let the engine spin, John. Ride it in the higher rev range - keep it above 5,000 rpm for a while." I did exactly that on the long ride home from my course, and after 30- 40 minutes the feel of the engine suddenly changed. Like throwing a switch to make everything feel looser and more responsive. This was on the 1100, but i did the same thing on the 1300 every now and then, to good effect. This too improved the pinking.
And then, after a few years, it just stopped doing it. I dont remember when - i guess around 40,000 miles.
This is all from memory. But i can look up the details if you want, i still have my records. I have never had any of these issues on my A9. After 2008, the Ecu was changed, and the engine has much more usable power at lower revs, and i dont have to take uphill hairpins with my fingers feathering the clutch. It just turns in and powers out, like - well, like the 1100 !
Not saying this is the same as your situation, but it may be related.