Your IIS does not support CCS, so the app is technically correct. Probably the old version let you write out the PFX to the folder anyway, but you weren't using it via CCS on that machine. CCS requires SNI to match certs to sites, which isn't available on Windows Server before 2012. I'm guessing you are probably not load balancing across multiple servers (are you?), which is what CCS is for.
As @_az suggested you should just use the local computer certificate store (the default) or just use the option to write out a file (win-acme).
You also need to urgently move your stuff to a newer version of Windows Server as Server 2008 R2 is not supported by Microsoft and is not receiving security updates, unless you have made special arrangements with Microsoft for extended support.