Chris,

I had what seemed like identical symptoms that you are experiencing.  My problems started when I switched from a self-signed web server certificate to a CA signed certificate.  Whilst the web interfaces functioned as normal, the iFolder 3 client for Windows x64 (running on Windows 7) would not connect to the server.  My Mac OS X client was unaffected.

The Windows client had previously connected but stopped almost as soon as I made the switch with the certificates.  Looking at the iFolder client logs, it seemed that the client was simply timing out; I was convinced it was because of the new certificate I'd installed.  I tried numerous things including generate a new certificate from a different CA and completely un-installing and reinstalling the client software.  Nothing worked.

However, the solution was, for me, much more trivial in the end.  I noticed that the apache error log was always logging the warning "RSA server certificate CommonName (CN) 'fqdn' does NOT match server name!?".  This seemed to be inconsequential so I had ignored it but in my desperation to find a solution to the client connectivity problem I decided to fix it: I uncommented the ServerName directive in the /etc/apache2/vhosts.d/vhost-ssl.conf file and entered the FQDN of the server and restarted apache.  I then entered the URL https://fqdn:443/ into the set up dialog of the iFolder client.  Lo and behold - the client connected.

I don't know if this will actually help you but since it worked for me it might give you a clue about where else to look.