(I thought I sent this but I guess I didn't so let me try again.)
I tried the Net::FTP package and the mdtm method and that did return the seconds. But, if I use the Net::FTP package I would lose my ability to get a list of files that match a file name pattern, like you can do with the Win32::Internet package's List method.
What I could do is still use the Win32::Internet List method to get the list of files but then use the Net::FTP package to log on to the FTP server (again) and use the mdtm method to get the modification time with the seconds, passing in the file name. Its kind of a hack but it should work.
I am glad that this Net::FTP idea is working out well for your application!
The Net::FTP package also has a way to get a list of files. You can use Perl grep{} to get a subset of file to make further queries upon. I don't see the need to mix Win32::Internet and Net::FTP.