Index: trunk/src_plugins/io_pcb/parse_l.c
===================================================================
--- trunk/src_plugins/io_pcb/parse_l.c	(revision 30924)
+++ trunk/src_plugins/io_pcb/parse_l.c	(revision 30925)
@@ -2775,6 +2775,8 @@
 
 	if ((settings_dest != CFR_invalid) && (retval == 0)) {
 		/* overwrite settings from the flags, mark them not-to-save */
+		pcb_conf_reset(settings_dest, "<io_pcb_ParsePCB>");
+		pcb_conf_main_root_replace_cnt[settings_dest]++;
 		CONF_SET(settings_dest, "plugins/mincut/enable", -1, CONF_BOOL_FLAG(PCB_ENABLEPCB_FLAG_MINCUT, yy_pcb_flags), POL_OVERWRITE);
 		CONF_SET(settings_dest, "editor/show_number", -1, CONF_BOOL_FLAG(PCB_SHOWNUMBERFLAG, yy_pcb_flags), POL_OVERWRITE);
 		CONF_SET(settings_dest, "editor/show_drc", -1, CONF_BOOL_FLAG(PCB_SHOWPCB_FLAG_DRC, yy_pcb_flags), POL_OVERWRITE);
Index: trunk/src_plugins/io_pcb/parse_l.l
===================================================================
--- trunk/src_plugins/io_pcb/parse_l.l	(revision 30924)
+++ trunk/src_plugins/io_pcb/parse_l.l	(revision 30925)
@@ -392,6 +392,8 @@
 
 	if ((settings_dest != CFR_invalid) && (retval == 0)) {
 		/* overwrite settings from the flags, mark them not-to-save */
+		pcb_conf_reset(settings_dest, "<io_pcb_ParsePCB>");
+		pcb_conf_main_root_replace_cnt[settings_dest]++;
 		CONF_SET(settings_dest, "plugins/mincut/enable", -1, CONF_BOOL_FLAG(PCB_ENABLEPCB_FLAG_MINCUT, yy_pcb_flags), POL_OVERWRITE);
 		CONF_SET(settings_dest, "editor/show_number", -1, CONF_BOOL_FLAG(PCB_SHOWNUMBERFLAG, yy_pcb_flags), POL_OVERWRITE);
 		CONF_SET(settings_dest, "editor/show_drc", -1, CONF_BOOL_FLAG(PCB_SHOWPCB_FLAG_DRC, yy_pcb_flags), POL_OVERWRITE);