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.
The following URLs are supported in Vibe, and might appear in the table above.
Permalinks are URLs that remain constant over time, and are used to reference individual workspaces, folders and entries. You can use them as bookmarks, or e-mail them to others. Copy and paste them as needed.
If the folder owner has set up an e-mail address for this folder, then you can add entries directly into the folder via e-mail.
Use the WebDAV URL to access a folder directly as a file directory. Applications such as Windows Explorer and Microsoft Office can use a WebDAV URL to directly access the files stored in a Vibe folder.
You can use this URL to synchronize Vibe task and calendar folders to your desktop calendar application.
Folders can also be accessed using an RSS or ATOM Feed Reader or directly from the file system. Copy the RSS URL below and paste it into your RSS reader to access this folder as an RSS feed.
Caution: This RSS URL has been created for your use only. It uses your access rights. Sending this URL to other people may give them access to entries in this folder that they may not otherwise be able to view.