You could try using a custom action in NetChk to push out the Flash Uninstaller to see if this helps. Then afterward you should be able to scan again with NetChk, then push out Flash (You may need to use a software distribution scan if Flash is not installed at all).
The Flash uninstaller can be found at http://download.macromedia.com/pub/flashplayer/current/uninstall_flash_player.exe.
Directions on how to set up a custom action in NetChk can be found in the Help section:
Help > Contents > Agentless Patch Management Tasks > Deployment Templates > Deployment Template: Custom Actions Tab.
I hope this helps!