This is a very annoying bug. Here is a workaround: By running the commands below in a terminal window, a small script and a configuration file is written to swap the tap action into a right-click at desktop startup, which is then swapped back into a left-click when the mouse is configured. (I have the lower left corner as right-click).
sudo sh -c 'cat > /usr/local/bin/set-left-tap.sh' <<'EOF'
# Reconfigure touchpad to report tap actions as right-click
# and lower-corner tap as left-click, which will subsequently
# be switched by the left-hand mouse configuration into left
# and right clicks, respectively.
# get a list of input devices that are mouse pointers, and process each of them
for id in $(xinput --list --short | grep "\[slave\ \ pointer\ \ ([0-9]*)\]" | sed -n "s,.*\tid=\([0-9]*\)\t.*,\1,p" | xargs); do
# get the id of the tap action property of this mouse
tap=$(xinput --list-props 10 | sed -n "s,.*\ Tap Action\ (\([0-9]*\)):.*,\1,p")
# only touchpads have tap actions, and those are the devices that we want to change
if [ -n "$tap" ]; then
# reconfigure the tap action (8 is the number of bits in each number)
# according to `man synaptics` section "Synaptics Tap Action", the
# order of the numbers are first tap in each of the four corners,
# followed by from one to three finger clicks on the pad surface
# we must set the assignment to opposite of what we want it to end up
# as, since the left-hand configuration will swap the button assignment
xinput set-prop --type=int --format=8 $id $tap 0 0 0 1 3 0 0
sudo chmod 755 /usr/local/bin/set-left-tap.sh
cat > ~/.config/autostart/set-left-tap.desktop <<'EOF'
Comment=Swap Touchpad Tap Action