I've just completed a tool that should fix the Materializing Materials issue on packages.
Just drag and drop your packages on top of the MMFixer.exe file and it should process them. There is a limit of about 30 to 50 packages (depends on the length of the filename) so be sure and do them in fairly small chunks.
This process doesn't modify ANYTHING except patterns that have the MM issue, so it is safe to run all of your packages through it. It also makes a backup copy of your original package file just in case something goes wrong.
It WILL NOT work on Sims3pack files, so you will need to use a sims3pack unpacker (See MTS or google) to be able to fix patterns that are inside a sims3pack.
Download at Sims 3 Stuff n Things