Thanks everyone for coming back with such helpful information.
As soon as I saw your post, Mont, the penny dropped. Your description fits the symptoms I'm seeing. Sure enough, in effect I have a low level "netting" tone that as you and Gregg describe must surely be caused by an internal signal leaking somehow from the Si5351 at the (intended next) transmit frequency.
If I lock my sign gen feeding -110dBm at the antenna socket to zero beat with the rogue "netting signal", then go to split mode, I hear a strong beat note at the difference between A and B frequencies.
Two potential "fixes" came to mind - the "Move Clk2 frequency well away during Rx" that Mont describes or, potentially, remove the resistor that feeds CLK2 alignment signal to the antenna input. There again, as Gregg found and Mont confirms, there's no signal actually at the CLK2 pin - so that may not work (but still might due to pick up along the track).
Daniel - good question regarding other ICs etc - my 74ACT00 voltages seem fine and it seems to be working OK. Similarly the processor volts are OK and it seems to be doing its stuff re display, ADC, keying, sidetone, CW reader,and so on. D1 and D2 are fine. When I killed the voltage regulator I had only 8V at the supply socket, so ~7.3V? ended up on the 5V rail. I think all the ICs bar the Si5351 are specified to tolerate 7V max (another of several "if only" thoughts that haunt me!). I'd expected the Si5351 to fail on account of, what, nearly 6V applied to it. It's still possible I suppose that the (I'm assuming for now) internal Tx freq signal is the stronger on account of some damage done; but that seems a bit subtle for a failure. Similarly maybe the 74ACT00 switching is a little less clean on the gate that feeds the alignment signal to the antenna (but again that would only be an issue if the assumed Tx signal is propogated along that route). I'm still wating to come across some subtle failure - with fingers crossed that my mini's all now as good as it can be :o)
Finally a big thanks, Hans, for your comments - as you say, not a critical issue. I hope that dust settles for you soon and that calm descends peacefully upon your shoulders.
Best wishes all
"When you understand the inside the outside will be just fine"