Their forums database is listed on Google's possible malware infected pages now but it says it has only been flagged once.
It has to be third party, most likely coming through ads. If you are patched you have nothing to worry about. The Windower files itself should not have been infected. Ads come from a totally different site which helps pays for the web hosting service -- windower is totally free after all.
Scragg posted the MD5 for the file, as long as that hasn't changed the file is still legit. I just downloaded the installer file and checked it myself; it's still good.
You can download free WinMD5 and check it yourself too -- which you should do anyways with most files downloaded ;)