In the other thread, they are using the SFTP protocol which you can make FIPS compliant.
Because you are using FTPS, which uses SSL/TLS, this isn't possible - MD5 is embedded as part of the SSL, TLS1.0 and TLS 1.1 protocols, which are what is supported by edtFTPnet/PRO.
TLS is actually FIPS compliant and is permitted to use MD5 (see FIPS 140-2 IG, D.8 [pg. 157, point (e)(1).]) , but your FIPS compliant mode simply disables MD5 which causes the problem.
At some point we will implement TLS 1.2, which will remove dependence on MD5.