diff --git a/src/avr.c b/src/avr.c
index 55542f438..0ac0f7837 100644
--- a/src/avr.c
+++ b/src/avr.c
@@ -614,6 +614,20 @@ double avr_timestamp() {
   return avr_ustimestamp()/1e6;
 }
 
+/*
+ * Initialize the global context pointer cx.
+ *
+ * This must be called once at program startup (with a NULL argument),
+ * and at each (re-)initialization of a programmer (with the
+ * respective programmer as argument).
+ */
+void init_cx(PROGRAMMER *pgm) {
+  if (pgm)
+    pgm->flag = 0;              // Clear out remnants of previous session(s)
+  mmt_free(cx);
+  cx = mmt_malloc(sizeof *cx);  // Allocate and initialise context structure
+  (void) avr_ustimestamp();     // Base timestamps from program start
+}
 
 int avr_read_byte_silent(const PROGRAMMER *pgm, const AVRPART *p, const AVRMEM *mem,
   unsigned long addr, unsigned char *datap) {
diff --git a/src/libavrdude.h b/src/libavrdude.h
index a3c04c056..3b7414198 100644
--- a/src/libavrdude.h
+++ b/src/libavrdude.h
@@ -1183,6 +1183,8 @@ uint64_t avr_mstimestamp(void);
 
 double avr_timestamp(void);
 
+void init_cx(PROGRAMMER *pgm);
+
 int avr_write_byte(const PROGRAMMER *pgm, const AVRPART *p, const AVRMEM *mem,
                    unsigned long addr, unsigned char data);
 
diff --git a/src/libavrdude.i b/src/libavrdude.i
index a4204dc86..8efc82eb9 100644
--- a/src/libavrdude.i
+++ b/src/libavrdude.i
@@ -53,15 +53,6 @@ static PyObject *msg_cb = NULL;
 static PyObject *progress_cb = NULL;
 static void swig_progress(int percent, double etime, const char *hdr, int finish);
 
-#define mmt_malloc(n) cfg_malloc(__func__, n)
-#define mmt_free(p) free(p)
-
-void init_cx(void) {
-  mmt_free(cx);
-  cx = mmt_malloc(sizeof *cx);  // Allocate and initialise context structure
-  (void) avr_ustimestamp();     // Base timestamps from program start
-}
-
 void set_msg_callback(PyObject *PyFunc) {
   if (PyFunc == Py_None) {
     if (msg_cb)
@@ -267,8 +258,6 @@ typedef struct avrmem_alias AVRMEM_ALIAS;
 typedef struct programmer PROGRAMMER;
 typedef void pgm_initpgm(PROGRAMMER*);
 
-void init_cx(void);
-
 enum msglvl {
   MSG_EXT_ERROR = (-3),         // OS-type error, no -v option, can be suppressed with -qqqqq
   MSG_ERROR = (-2),             // Avrdude error, no -v option, can be suppressed with -qqqq
@@ -599,6 +588,8 @@ typedef struct programmer {
 %mutable;
 %clear struct programmer *pgm;
 
+void init_cx(PROGRAMMER *pgm = NULL);
+
 // Config file handling
 int init_config(void);
 
diff --git a/src/main.c b/src/main.c
index a43a3aa30..427788942 100644
--- a/src/main.c
+++ b/src/main.c
@@ -663,8 +663,7 @@ int main(int argc, char * argv [])
   char  * logfile;     /* Use logfile rather than stderr for diagnostics */
   enum updateflags uflags = UF_AUTO_ERASE | UF_VERIFY; /* Flags for do_op() */
 
-  cx = mmt_malloc(sizeof *cx);  // Allocate and initialise context structure
-  (void) avr_ustimestamp();     // Base timestamps from program start
+  init_cx(NULL);
 
 #ifdef _MSC_VER
   _set_printf_count_output(1);
diff --git a/src/python/adgui.py b/src/python/adgui.py
index 4fef35ba9..56680d0e0 100755
--- a/src/python/adgui.py
+++ b/src/python/adgui.py
@@ -935,7 +935,7 @@ def loglevel_changed(self, checked: bool):
     def start_programmer(self):
         if self.connected:
             return
-        ad.init_cx()
+        ad.init_cx(self.pgm)
         self.pgm.initpgm()
         self.pgm.setup()
         rv = self.pgm.open(self.port)