diff --git a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
index ffa87055621b1bbbe9dd4b96b80723dc43cc8bf0..58a6f77f4edfde3a40f6266c26d8cf0898af4b99 100644
--- a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
+++ b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
@@ -2,7 +2,7 @@
 # 'ms-injection' drop box for spectra data
 # ---------------------------------------------------------------------------
 # The directory to watch for incoming data.
-incoming-dir = ${data-dir}/incoming-ms-injection
+incoming-dir = ${incoming-root-dir}/incoming-ms-injection
 
 # Determines when the incoming data should be considered complete and ready to be processed.
 # Allowed values: 
diff --git a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
index 7773492161f75af08a7804c0ffc9376ada75ecf7..b39ac151edb6f1d9176e36c6c105a9b1e685f6be 100644
--- a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
+++ b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
@@ -1,7 +1,7 @@
 # ---------------------------------------------------------------------------
 # 'ms-search' drop box for protein data
 # ---------------------------------------------------------------------------
-incoming-dir = ${data-dir}/incoming-ms-search
+incoming-dir = ${incoming-root-dir}/incoming-ms-search
 
 incoming-data-completeness-condition = auto-detection
 
diff --git a/rtd_phosphonetx/dist/etc/service.properties b/rtd_phosphonetx/dist/etc/service.properties
index c09174beed1b500aadb2ef346e39a1eb05023b25..61f0f91828a6ad109309c8cd7941391301885286 100644
--- a/rtd_phosphonetx/dist/etc/service.properties
+++ b/rtd_phosphonetx/dist/etc/service.properties
@@ -7,7 +7,9 @@ host-address = https://localhost
 data-dir = ../data
 
 # The root directory of the data store
-storeroot-dir = ${data}/store
+storeroot-dir = ${data-dir}/store
+
+incoming-root-dir = ${data-dir}
 
 # The directory where the command queue file is located; defaults to storeroot-dir 
 commandqueue-dir =
diff --git a/rtd_phosphonetx/dist/tarball/installer/dss-service.properties b/rtd_phosphonetx/dist/tarball/installer/dss-service.properties
index 1a9fcc16137dd2aa43029ebd80ccaf6b81945ae6..3aef05287ba5b7eefa2d9914a6d525fe6c49698e 100644
--- a/rtd_phosphonetx/dist/tarball/installer/dss-service.properties
+++ b/rtd_phosphonetx/dist/tarball/installer/dss-service.properties
@@ -4,11 +4,10 @@
 
 root-dir = $DSS_ROOT_DIR
 storeroot-dir = ${root-dir}/store
+incoming-root-dir = ${root-dir}
 
 host-address = https://$HOSTNAME
 quiet-period = 10
 check-interval = 5
 
-data-dir = ${root-dir}
-
 core-plugins-folder = ../core-plugins
\ No newline at end of file