I went ahead and tried this...

I just downloading this title here from download.com:


Using IE9 with Smartscreen filter "ON"

The only pop up I got was "Do you want run or save pc_check_tuning_2012_81mb_us.exe (80.3MB) from software-files-a.cnet.com"

I clicked "Save" and IE did it's security checked and it passed and I saved the file and was able execute the file and ran the software with no flags.

Are you using IE9 or 8?