JSCAPE MFT Server is a Java based product therefore the ciphers used for encryption are those that are provided by the JVM. Sun/Oracle does not currently provide a FIPS validated JVM however they do provide instructions on pointing to a FIPS provider. See the following:
IBM provides a FIPS certified JVM that can also be used with JSCAPE MFT Server.
While the ciphers that are used by default Sun/Oracle JVM are not FIPS validated you can control the ciphers that are used by JSCAPE MFT Server to only use FIPS recognized ciphers. Ciphers for each of the protocols can be set in the following panels:
FTPS - Services > FTP/S > SSL/TLS Ciphers
HTTPS/AS2 - Server > Settings > Web > SSL/TLS Ciphers
SFTP - Services > SFTP > Algorithms > Ciphers