This is my workaround to get clamwin to scan after downloads with FreshDownload:

On the download completion tab in the options window:
1. check the box for virus checking
2. in the virus scanner box enter:
C:\Program Files\ClamWin\bin\ClamWin.exe
(No quotation marks or truncated folder names are necessary. Substitute the correct path if this is not where your clamwin is installed.)
3. in the parameter box enter:
--mode=scanner --path="C:\Documents and Settings\Default\My Documents\My Downloads"
(USE quotation marks here! Substitute the correct path to your download directory.)

This method will scan the entire *specified* directory everytime a download completes. Of course this is useless if you don't download all files to the same directory. I haven't been able to get the darn thing to actually scan only the file or scan regardless of the directory.

Please note, I have only gotten this to work through trial and error. My OS is XP Home SP2, I'm using clamwin 0.94.1 and FreshDownload 8.14. Your mileage may vary.

-Glenda