I had a similar experience of the knocking sound, especially with humps and bumpy roads. But this was only after i installed my set of TRD lowering springs from US and not with my stock set.

Numerous adjustments, re installation, hose insulation didn't do the trick. It was only after we inspected the shock mount assembly and found out that the ring washer was too loose and not thick enough to give grip even when fully tightened.

My mechanic even showed me that the shock assembly parts are not entirely from japan and the said part was made in china. I found that weird but didn't bother to post in other forums or report to toyota in my last pms.

After we have replaced it with an after market type and installed on both sides, i never encountered the problem again.

We even subjected the altis at various humps and bumpy roads with minimal braking, and there were no more annoying knocking sounds till now.

TMP maybe right, that after a few thousand kilometers accrued, even the stock suspension and spring will somehow settle. This also the same principle if you put a lowering spring. And with that faulty ring, various users will eventually experience the knocking sound.

Hope this helps.