You can't assign a process output directly into a var, you need to parse the output with a For /F loop:
@Echo OFF
FOR /F "Tokens=2,*" %%A IN (
'Reg Query "HKEY_CURRENT_USER\Software\Macromedia\FlashPlayer" /v "CurrentVersion"'
) DO (
REM Set "Version=%%B"
Echo Version: %%B
)
Pause&Exit
PS: Change the reg key used if needed.