Changed "~" to "$HOME" for JEKYLL_LOCAL_ROOT variable. Sometimes ~ works, sometimes not. I know for a fact that $HOME does though.
diff --git a/template/bash_profile.template.bash b/template/bash_profile.template.bash
index 31e6645..a98e65c 100644
--- a/template/bash_profile.template.bash
+++ b/template/bash_profile.template.bash
@@ -28,7 +28,7 @@
# Change this to the path of your local jekyll root to use the jekyll aliases
-export JEKYLL_LOCAL_ROOT="~/Sites/jekyllsite"
+export JEKYLL_LOCAL_ROOT="$HOME/Sites/jekyllsite"
# And change this to the remote server and root