Sounds strange, for Shockwave and Flash can you check the following folders exist after ghosting:
C:\Windows\System32\Macromed\Flash
C:\Windows\System32\Macromed\Shockwave 10
Sysprep shouldn't be removing these files as they are independant of the operating system. It makes me wander if the applications were installed in per user mode rather than per machine mode, which would explain why they wouldn't appear for new users? Just a thought anyway.
Cheers