If GBArunner2 is still booting, that means that you haven't edited "settings.ini" Please copy and paste your file here so we can see what's wrong. BTW nothing related to GBArunner3 will appear on TM++ settings menu yet.
Haha nice, I wasn't aware that GBARunner2 was hanging on this place, I never got that far using it lol.
SRLOADER]
GBARUNNER3_TEST = 1
ROM_FOLDER = sd:/
INITIAL_ROM_FOLDER = null
SECONDARY_ROM_FOLDER = fat:/!GBA HOMEBREW
INITIAL_SECONDARY_ROM_FOLDER = null
PAGE_NUMBER = 0
SECONDARY_PAGE_NUMBER = 0
CURSOR_POSITION = 0
SECONDARY_CURSOR_POSITION = 0
CONSOLE_MODEL = 0
LANGUAGE_SET = 1
REGION_SET = 1
LOGGING = 0
LANGUAGE = -1
TITLELANGUAGE = 1
FRAME_RATE = 60
MACRO_MODE = 0
COLOR_MODE = Default
DSIWARE_EXPLOIT = 0
WIFI_LED = 1
WIFI_LED_VER = 1
POWER_LED_COLOR = 0
SD_REMOVE_DETECT = 1
SHOW_MICROSD = 0
GBAR2_DLDI_ACCESS = 0
SHOW_MAIN_MENU = 0
SHOW_SELECT_MENU = 1
THEME = 0
SETTINGS_MUSIC = -1
DSI_MUSIC = 3
PHOTO_BOXART_COLOR_DEBAND = 0
SHOW_GBA = 1
SHOW_COL = 2
SHOW_SG = 2
SHOW_CPC = 1
SHOW_MDGEN = 1
UPDATE_RECENTLY_PLAYED_LIST = 1
SORT_METHOD = 1
HIDE_EMPTY_BOXES = 1
SHOW_DIRECTORIES = 1
SHOW_HIDDEN = 0
SHOW_PHOTO = 0
SHOW_BOX_ART = 0
ROCKET_ROBZ_LOGO = 0
ANIMATE_DSI_ICONS = 1
SHOW_CUSTOM_ICONS = 1
PREVENT_ROM_DELETION = 0
SYS_REGION = -1
LAUNCHER_APP = -1
SECONDARY_ACCESS = 0
PREVIOUS_USED_DEVICE = 1
SAVE_LOCATION = 1
SLOT1_LAUNCHMETHOD = 1
DSI_SPLASH = 0
DSI_SPLASH_AUTO_SKIP = 0
NINTENDO_LOGO_COLOR = 1
SHOWLOGO = 0
LONG_SPLASH_JINGLE = 0
AUTORUNGAME = 0
AUTORUNSLOT1 = 0
SHOW_12H_CLOCK = 1
R4_THEME = unused
DSI_THEME = Windows 95
3DS_THEME = light
GBA_BORDER = default.png
UNLAUNCH_BG = default.gif
UNLAUNCH_LAUNCHER_PATCHES = 2
FONT = default
USE_THEME_FONT = 1
DS_CLASSIC_CUSTOM_FONT = 0
DONT_SHOW_CLUSTER_WARNING = 0
IGNORE_BLACKLISTS = 0
SLOT1_ENABLESD = 0
SLOT1_SCFG_UNLOCK = 0
SLOT1_TOUCH_MODE = 0
LIMITED_MODE = 0
DONT_SHOW_DSIWARE_IN_DS_MODE_WARNING = 0
DSIWARE_BOOTER = 1
DSIWARE_TO_SD = 1
SMS_GG_IN_RAM = 0
ESRB_RATING_SCREEN = 0
AK_VIEWMODE = 2
AK_THEME = zelda
AK_ZOOM_ICONS = 1
USE_BOOTSTRAP = 1
BOOTSTRAP_BOOTLOADER_DIRECT = 0
BOOTSTRAP_FILE = 0
INTERNET_BROWSER_LAUNCHED = 0
SLOT1_LAUNCHED = 0
LAUNCH_TYPE = 0
SECONDARY_LAUNCH_TYPE = 17
HOMEBREW_BOOTSTRAP = 1
HOMEBREW_HAS_WIDE = 0
WIDESCREEN = 0
SECONDARY_ROM_PATH = fat:/!GBA GAMES/Drill Dozer.gba
SECONDARY_HOMEBREW_ARG = fat:/!GBA GAMES/Drill Dozer.gba
[NDS-BOOTSTRAP]
LANGUAGE = 1
REGION = 3
USE_ROM_REGION = 1
EXTENDED_MEMORY = 0
FORCE_SLEEP_PATCH = 0
SOUND_FREQ = 0
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SECONDARY_HOMEBREW_ARG = fat:/!GBA GAMES/Kirby - Nightmare in Dreamland.gba
HOMEBREW_BOOTSTRAP = 1
HOMEBREW_HAS_WIDE = 0
WIDESCREEN = 0
[SRLOADER]
ROM_FOLDER = sd:/
INITIAL_ROM_FOLDER = null
SECONDARY_ROM_FOLDER = fat:/!DS HOMEBREW
INITIAL_SECONDARY_ROM_FOLDER = null
SECONDARY_ROM_PATH = fat:/!DS HOMEBREW/HmBrw, poptire.nds
PAGE_NUMBER = 0
SECONDARY_PAGE_NUMBER = 0
CURSOR_POSITION = 0
SECONDARY_CURSOR_POSITION = 19
CONSOLE_MODEL = 0
LANGUAGE_SET = 1
REGION_SET = 1
LOGGING = 0
LANGUAGE = -1
TITLELANGUAGE = 1
FRAME_RATE = 60
MACRO_MODE = 0
COLOR_MODE = Default
DSIWARE_EXPLOIT = 0
WIFI_LED = 1
WIFI_LED_VER = 1
POWER_LED_COLOR = 0
SD_REMOVE_DETECT = 1
SHOW_MICROSD = 0
GBAR2_DLDI_ACCESS = 0
SHOW_MAIN_MENU = 0
SHOW_SELECT_MENU = 1
THEME = 0
SETTINGS_MUSIC = -1
DSI_MUSIC = 3
PHOTO_BOXART_COLOR_DEBAND = 0
SHOW_GBA = 1
SHOW_COL = 2
SHOW_SG = 2
SHOW_CPC = 1
SHOW_MDGEN = 1
UPDATE_RECENTLY_PLAYED_LIST = 1
SORT_METHOD = 1
HIDE_EMPTY_BOXES = 1
SHOW_DIRECTORIES = 1
SHOW_HIDDEN = 0
SHOW_PHOTO = 0
SHOW_BOX_ART = 0
ROCKET_ROBZ_LOGO = 0
ANIMATE_DSI_ICONS = 1
SHOW_CUSTOM_ICONS = 1
PREVENT_ROM_DELETION = 0
SYS_REGION = -1
LAUNCHER_APP = -1
SECONDARY_ACCESS = 0
PREVIOUS_USED_DEVICE = 1
SAVE_LOCATION = 1
SLOT1_LAUNCHMETHOD = 1
DSI_SPLASH = 0
DSI_SPLASH_AUTO_SKIP = 0
NINTENDO_LOGO_COLOR = 1
SHOWLOGO = 0
LONG_SPLASH_JINGLE = 0
AUTORUNGAME = 0
AUTORUNSLOT1 = 0
SHOW_12H_CLOCK = 1
R4_THEME = unused
DSI_THEME = Windows 95
3DS_THEME = light
GBA_BORDER = default.png
UNLAUNCH_BG = default.gif
UNLAUNCH_LAUNCHER_PATCHES = 2
FONT = default
USE_THEME_FONT = 1
DS_CLASSIC_CUSTOM_FONT = 0
DONT_SHOW_CLUSTER_WARNING = 0
IGNORE_BLACKLISTS = 0
SLOT1_ENABLESD = 0
SLOT1_SCFG_UNLOCK = 0
SLOT1_TOUCH_MODE = 0
LIMITED_MODE = 0
DONT_SHOW_DSIWARE_IN_DS_MODE_WARNING = 0
DSIWARE_BOOTER = 1
DSIWARE_TO_SD = 1
SMS_GG_IN_RAM = 0
ESRB_RATING_SCREEN = 0
AK_VIEWMODE = 2
AK_THEME = zelda
AK_ZOOM_ICONS = 1
USE_BOOTSTRAP = 1
BOOTSTRAP_BOOTLOADER_DIRECT = 0
BOOTSTRAP_FILE = 0
INTERNET_BROWSER_LAUNCHED = 0
SLOT1_LAUNCHED = 0
LAUNCH_TYPE = 0
SECONDARY_LAUNCH_TYPE = 2
SECONDARY_HOMEBREW_ARG = fat:/!GBA GAMES/Pac-Man Collection.gba
HOMEBREW_BOOTSTRAP = 1
HOMEBREW_HAS_WIDE = 0
WIDESCREEN = 0