Also, when I try opening the Arduino IDE the top and bottom of the window are out of the screen so I can't resize it and use it normally.
I've tried modifying the config.txt file and this did not address the problems mentioned above. I forced the screen resolution to my real resolution and this didn't produce any differences.
Here's my config.txt file if it helps =>
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# uncomment if you get no picture on HDMI for a default "safe" mode #hdmi_safe=1 # uncomment this if your display has a black border of unused pixels visible # and your display can output without overscan disable_overscan=1 # uncomment the following to adjust overscan. Use positive numbers if console # goes off screen, and negative if there is too much border #overscan_left=16 #overscan_right=16 #overscan_top=16 #overscan_bottom=16 # uncomment to force a console size. By default it will be display's size minus # overscan. framebuffer_width=640 framebuffer_height=480 # uncomment if hdmi display is not detected and composite is being output #hdmi_force_hotplug=1 # uncomment to force a specific HDMI mode (this will force VGA) hdmi_group=1 hdmi_mode=1 # uncomment to force a HDMI mode rather than DVI. This can make audio work in # DMT (computer monitor) modes #hdmi_drive=2 #uncomment to overclock the arm. 700 MHz is the default. #arm_freq=800 # for more options see http://elinux.org/RPi_config.txt