The dashes need escaped even though they are quoted.

rc_shared.sh

@@ -86,7 +86,7 @@ function today { date "+%Y%m%d"; }
 
 function send-masters {
    echo -e "`date` - Looping through MASTER directories.\n"
-   ls | grep '-MASTER' | while read dir; do
+   ls | grep '\-MASTER' | while read dir; do
       echo -e "`date` - Found '$dir'..."
       cd $dir
       send-master
@@ -97,7 +97,7 @@ function send-masters {
 
 function pull-clones {
    echo -e "`date` - Looping through clone directories.\n"
-   ls | grep '-clone' | while read dir; do
+   ls | grep '\-clone' | while read dir; do
       echo -e "`date` - Found '$dir'..."
       cd $dir
       pull-clone