Reloading doesn't respect bottom padding on second monitor

[promitheas17j]

When reloading the config using the sxhkd binding, often bspwm seems to ignore the bottom padding assigned to windows of the second monitor, leading to a rather large gap below them.

Screenshot with red line roughly where my monitors are separated

I have my secondary monitor above my primary, and in the screenshot above I drew a red line to represent roughly where one ends and the other begins.

Here is my bspwmrc:

#! /bin/sh

# pgrep -x sxhkd > /dev/null || sxhkd -s &
# pgrep -io "sxhkd" || { killall sxhkd; sxhkd > /dev/null 2>&1 & }
pgrep -io "sxhkd" | xargs kill
sxhkd -s &

pgrep -x copyq > /dev/null || copyq &
pgrep -x xfce4-power-manager > /dev/null || xfce4-power-manager &
pgrep -x dunst > /dev/null || dunst &
pgrep -x nm-applet > /dev/null || nm-applet &

pgrep -x picom > /dev/null | xargs kill
picom -b

pgrep -x polybar > /dev/null | xargs kill
$HOME/.config/polybar/launch.sh

# $HOME/.fehbg &
# On startup, bottom monitor's background is stretched and generally looks bad (its just a bunch of lines), until I restart my bspwm session. Placing the feh command a second time to test if this solves it.
# $HOME/.fehbg & 

setxkbmap us
$HOME/.bin/remap-caps-esc

bspc config border_width         2
bspc config window_gap           10
# bspc config 

bspc config split_ratio          0.52
bspc config borderless_monocle   true
bspc config gapless_monocle      true

# Dracula theme
bspc config normal_border_color "#44475a"
bspc config active_border_color "#6272a4"
bspc config focused_border_color "#8be9fd"
bspc config presel_feedback_color "#6272a4"

sleep 3
xrandr --auto
connected_monitors=$(xrandr --listmonitors | grep "^Monitors:" | cut -d' ' -f2)
if [[ "$connected_monitors" -gt 1 ]];
then
	xrandr --output HDMI-A-0 --primary --mode 1920x1080 --pos 0x0 --rotate normal
	xrandr --output HDMI-A-1 --mode 1920x1080 --rotate inverted --above HDMI-A-0
	bspc monitor HDMI-A-0 -d 1 2 3 4 5
	bspc monitor HDMI-A-1 -d 6 7 8 9 0
	
	# pgrep -x polybar > /dev/null || $HOME/.config/polybar/launch.sh

	# Fix gap appearing above windows on first monitor after restarting bspwm
	bspc config -m HDMI-A-0 top_padding 3
	bspc config -m HDMI-A-0 bottom_padding 40
	
	# Fix top/bottom margins for secondary monitor
	bspc config -m HDMI-A-1 bottom_padding 3
	bspc config -m HDMI-A-1 top_padding 40

	bspc wm -O HDMI-A-0 HDMI-A-1
	$HOME/.fehbg & 
	xset s off
	xset s noblank
	xset -dpms
else
	monitor_name="$(xrandr --listmonitors | awk 'NR==2 {print $4}')"
	xrandr --output "$monitor_name" --scale 1.0x1.0 --mode 1920x1080 --primary
	# bspc monitor -d I II III IV V VI VII VIII IX X
	bspc monitor "$monitor_name" -d 1 2 3 4 5 6
	# xinput set-button-map 9 1 2 3 5 4 6 7
	xinput set-prop 'SYNA8007:00 06CB:CD8C Touchpad' 318 1
	# pgrep -x polybar > /dev/null || $HOME/.config/polybar/launch.sh
	$HOME/.fehbg & 
fi


# Make sure theme cursor is shown when mouse is not over a window, instead of the standard default one
xsetroot -cursor_name left_ptr

bspc rule -a Gimp desktop='^8' state=floating follow=on
bspc rule -a Chromium desktop='^2'
bspc rule -a mplayer2 state=floating
bspc rule -a Kupfer.py focus=on
bspc rule -a Screenkey manage=off
bspc rule -a Zathura state=tiled
bspc rule -a Passy state=tiled

bspc rule -a scpad sticky=on state=floating rectangle=1896x400+10+50

$HOME/.bin/parse_keybinds.sh
betterlockscreen -u $HOME/Pictures/wallpapers/ --fx dim --dim 50

eval $(ssh-agent)
SSH_ASKPASS=/usr/lib/ssh/x11-ssh-askpass ssh-add ~/.ssh/id_ed25519 < /dev/null

Sometimes, if I reload it a couple times it fixes itself, but this time it refuses to do so, no matter how many times I relaod it.

BSPWM version: bspwm 0.9.11-2
Kernel version: 6.17.1-arch1-1

Let me know if you would like more info and I'll provide it