Logon script not read: We have implemented the recommendations around performance improvement by enabling replication and the use of version number in both the Esession.txt file and the Elogon.txt file.
However, the logon script is not being read. I have stored it in the corresponding SAP MIME repository directory along with all the other scripts but it is being ignored completely, as if it didn't exist.
What am I doing wrong?
You are  probably using the "Script download via current client" option in GuiXT profile. In this case the logon script is not read, since the client is not known before the user has logged on.

If it is always the same client, e.g. client 100, you can use the notation

Directory1 SAPMR,client=100:SAP/PUBLIC/...

without the "Script download via current client" option, and the logon script will be read.