diff --git a/programmer/.gitignore b/programmer/.gitignore
index 25fe328..197949b 100644
--- a/programmer/.gitignore
+++ b/programmer/.gitignore
@@ -9,6 +9,10 @@ __pycache__/
 *~
 tinyprog/full_version.py
 
+# due to pip install . (for development)
+# https://github.com/pypa/pip/issues/6213
+pip-wheel-metadata
+
 # due to using tox and pytest
 .tox
 .coverage
diff --git a/programmer/tinyprog/__init__.py b/programmer/tinyprog/__init__.py
index 3648c38..9b673e0 100644
--- a/programmer/tinyprog/__init__.py
+++ b/programmer/tinyprog/__init__.py
@@ -114,9 +114,20 @@ def __str__(self):
         return self.port_name
 
     def __enter__(self):
+        # Timeouts:
+        # - Read:  2.0 seconds (timeout)
+        # - Write: 5.0 seconds (writeTimeout)
+        #
+        # Rationale: hitting the writeTimeout is fatal, so it pays to be
+        # patient in case there is a brief delay; readTimeout is less
+        # fatal, but can result in short reads if it is hit, so we want
+        # a timeout high enough that is never hit normally.  In practice
+        # 1.0 seconds is *usually* enough, so the chosen values are double
+        # and five times the "usually enough" values.
+        #
         try:
             self.ser = serial.Serial(
-                self.port_name, timeout=1.0, writeTimeout=1.0).__enter__()
+                self.port_name, timeout=2.0, writeTimeout=5.0).__enter__()
         except serial.SerialException as e:
             raise PortError("Failed to open serial port:\n%s" % str(e))
 
@@ -514,17 +525,36 @@ def program_sectors(self, addr, data):
                     minor_write_data = current_write_data[
                         minor_offset:minor_offset + minor_sector_size]
 
+                    # The TinyFPGA firmware and/or flash chip does not handle
+                    # partial minor sector writes properly, so pad out a final
+                    # write of a partial to a whole minor sector, if we are
+                    # writing aligned to the SPI flash internal minor sectors.
+                    #
+                    # Due to the way SPI flash works, writing 0xff *without
+                    # erasing* should be a no-opt, because 0xff is what you
+                    # get after erasing, and you can only write 0 bits.
+                    current_minor_addr = current_addr + minor_offset
+
+                    if (((current_minor_addr % minor_sector_size) == 0) and
+                        (len(minor_write_data) < minor_sector_size)):
+                         assert((current_minor_addr % minor_sector_size) == 0)
+
+                         pad_len = minor_sector_size - len(minor_write_data)
+                         padding = b'\xff' * pad_len
+
+                         minor_write_data = bytearray(minor_write_data)
+                         minor_write_data.extend(padding)
+                         assert(len(minor_write_data) == minor_sector_size)
+
                     # if the minor data is all 0xFF then it will match
                     # the erased bits and doesn't need to be re-sent
-                    if minor_write_data == chr(0xFF) * len(minor_write_data):
-                        pbar.update(len(minor_write_data))
-                        continue;
+                    if minor_write_data != chr(0xFF) * len(minor_write_data):
+                        self.write(
+                            current_addr + minor_offset,
+                            minor_write_data,
+                            disable_progress=True,
+                            max_length=256)
 
-                    self.write(
-                        current_addr + minor_offset,
-                        minor_write_data,
-                        disable_progress=True,
-                        max_length=256)
                     minor_read_data = self.read(
                         current_addr + minor_offset,
                         len(minor_write_data),