It seems none of the updates were integrated, despite me selecting a lot of them, including IE9.

I still have IE8 and Microsoft Update shows a bunch of available updates.

What could be the problem?

Attached the ini.

27-11-2011_22-02-43.ini

don't select LDR-QFE if u want to integrate IE 9 and its updates...

now place the updates in this order

KB982861

then KB2586448

and in last KB 2624899

if u will select LDR-QFE then niether IE9 and nor its updates will be integrated to win7 dvd..

No. Deleting all the settings and other files left from older versions of W7T solved the weird behavior for me.

Regarding IE9 and LDR-QFE:

BTW you only need the ie9 hotfix if you are forcing the LDR branch to install, because the main IE9 installer already has the updates