cipher is a MS built in app...
Hopefully the transfer is being done over a WebDAV share if you are using standard windows file sharing, otherwise you might want to look into that or FTP/SSH (sftp) or FTP/SSL (ftps) or something else to protect the data across the wire.
Anyways...
Here's the EFS crash course for admins:
http://technet.microsoft.com/en-us/library/bb457020.aspxNot sure what cert(s) got updated - I'm guessing the Data Recovery Agent (DRA)? If that's the case try looking at the local security policy (secpol.msc) - public key policy -and see if there is a DRA policy defined there and if so update that. You'll probably also want to install the certificate (from the .cer file, not .pfx) on each workstation as well - when installing choose to manually select the store, then when browsing checkmark the 'show physical stores' then expand Personal - Local computer
Afterwards you will need to run this command under each user context that has a valid efs cert on that box:
cipher /u
This will go through and update the efs certs for every efs encrypted file to use the new efs certs. This should be done regardless of if was the user's efs cert or if it was the DRA cert.
Since you are copying to the server, you will need to do the same on the server - since things are working for domain members this is why I'm assuming is probably the DRA that you updated via GPO?
If there wasn't a DRA then its not too late to start using one. Technically this is best issued from your CA and valid for about 5 years for a 2048 key strength. Issue to a specially created DRA account (don't use the domain admin or anyone else you may want to encrypt data with...) export the issued cert with the private key and back that up on flash drive or cd locked up - make a backup copy for offsite. That being said, many choose to to use cipher /r filename instead which will create a 99 year cert with the .cer and .pfx files already - again backup and lock up the .pfx file. In either case, delete the .pfx after backing up and validating it copied correctly.
If there's anything you're not sure of just let me know.