PPCGeeks - Kitchen updates changed my ROM build? Lost functions!

I've enjoyed using PPCKitchen on my old HTC Apache and now the Titan.
I worked through all the particular issues with being on the Telecom New Zealand network (saving and correcting the HDR username&password, and loading the Telecom carriers cab).
In short, I had upgraded to WM6.1 on my Titan with a decent custom ROM build which had been working for a few months.

But recently, I decided some of the apps were a bit memory hungry and/or leaked memory. So I decided to waste some more time trimming my build selection.
Of course, I let PPCKitchen do it's auto-update thing, then removed some selections and rebuilt the ROM.
When all was done, I found some of my favorite features were missing, so I rebuilt to the previous build selection. But still things were different...

Good change:
The Telecom carrier cab was already installed and my HDR values were remembered.

Bad changes:
I can no longer tap-drag to scroll around PIE
The Titan camera app didn't get installed
When I go to setup my Hotmail account to sync, it just directs me to live.com on PIE
Some icons in favorite web pages in PIE don't load

Has anyone had similar issues, or know how to correct these issues?
Cheers, Barnaby