Your IFS is set wrong. THe IFS="" says there is no separator so the whole file is read. You can only use IFS is there is actually a seperator between each field. So cat $FILE will not give you line by line it will give you the while file as a field at once. Hence only matching 1 time. Since you really want look at each line as a record you should use awk or sed to find and replace the text.

So this will work for you which was posted by devtakh which says search the whole file and replace the matching pattern with the given pattern for each instance you want to change. It will find each one separately and change the file the way you want.

sed '/Server=127.0.0.1/{s//Server=0.0.0.0/g}
/ServerPort=0/{s//ServerPort=1/g}
/Enable Server=1/{s//Enable Server=0/g}
' /opt/server.conf > /opt/new_server.conf