In case someone hasn't yet resolved this problem, here is the solution.
PROBLEM: If you install "gte2_core_update_eng_v581.exe" updater (pointing your game folder along the way), installer states "SUCCESS".
But when you want to apply "mtc80_sabow_patch_aug12_eng_beta3.gt2extension" patch, updater can't handle *.gt2extension files. It seems that updater, didn't really change anything and can't overwrite game files (being an admin does not help either).
SOLUTION:
1) Uninstall updater if installed
2) Install it again in temporary directory. We do this only to see file structure and find out which files need to be changed
3) Open side by side view, browse temp directory, find and rename all corresponding files in game file structure
4) Uninstall updater (don't delete temp folder, we don't want to leave mess in Control Panel)
5) Install Updater in Game folder again
Now success really is success, *.gt2extension can be handled.
Updater and patch can be found here:
http://graviteam.ua/help/download-patches.html