Changed the above settings to the suggestions and added:
$sessionOptions.FtpSecure = [WinSCP.FtpSecure]::ExplicitTls

In GUI you are obviously connected with FTP over TLS.
So you need to use the SessionOptions.SslHostCertificateFingerprint and set SessionOptions.Protocol to Ftp and SessionOptions.FtpSecure to Explicit (or ExplicitTls in older versions).
https://winscp.net/eng/docs/library_sessionoptions

I'm trying to transfer some files using the winscp.dll and receiving an exception on the fingerprint format.

This is the Server Options info I have from the winscp console.
#File transfer protocol = FTP
#Cryptographic protocol = TLS Explicit encryption, TLSv1.2
#Encryption algorithm = TLSv1/SSLv3: RC4-SHA, 2048 bit RSA
#Compression = No
#------------------------------------------------------------
#Certificate fingerprint
#78:b7:ed:6a:2a:6d:06:61:ae:7d:f6:e5:75:7c:0d:68:cc:aa:37:78

Here are some ways I've formatted the statements.
$sessionOptions.SshHostKeyFingerprint = "ssh-dss 2048 78:b7:ed:6a:2a:6d:06:61:ae:7d:f6:e5:75:7c:0d:68:cc:aa:37:78"
$sessionOptions.SshHostKeyFingerprint = "ssh-rsa 1024 78:b7:ed:6a:2a:6d:06:61:ae:7d:f6:e5:75:7c:0d:68:cc:aa:37:78"

This works but throws an error later saying it still needs a key.
$sessionOptions.SslHostCertificateFingerprint = "78:b7:ed:6a:2a:6d:06:61:ae:7d:f6:e5:75:7c:0d:68:cc:aa:37:78"

Not sure what I'm missing!

Thanks for help!