I had exactly this problem with an exe file that is downloadable from my web site. Whenever I tried to download the file using Chrome it gave the warning.
The solution I found was to sign up to Google Webmaster Tools and add my site. It took several days for Google to crawl my site, and fill in any information, but I went back today and finally found loads of information there.
Now I can download my file, and there is no malicious warning any more.
It seems that once Google has checked out your site and determined that you are not a bad person, the problem goes away.