Just tried r373 and no more odd graphics when loading or exiting games. Sweet!
I just tested emu mode and it didn't run an N64 game but exited to the main Wii screen. Here is my log:
Welcome to WiiFlow (Mod 3.1-r373)!
This is the debug output.
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Loading cIOS: 249
Reloading into IOS 249 from 58 (AHBPROT: 0)...
Going to show a wait message screen, delay: 15, # images: 5
OK, Current IOS: 249
Loaded cIOS: 249 has base 56
SECTORS: 3907029166
SEC SIZE: 512
HDD SIZE: 1.956 TB [512]
Wiiflow boot.dol Location: usb1:/apps/wiiflow
DML is not installed as MIOS
Loading cIOS map
Found base 56 in slot 249
Found base 57 in slot 250
Data Directory: usb1:/wiiflow
Loading files containing .ogg|.mp3 in usb1:/wiiflow/themes/DEFAULT/music
Loading music list from path: usb1:/wiiflow/themes/DEFAULT/music
Calling list to update filelist
Loading files containing .ogg|.mp3 in usb1:/wiiflow/music
Loading music list from path: usb1:/wiiflow/music
Calling list to update filelist
SHND: Running sound thread
Trying to open 'usb1:/wiiflow/settings/wiitdb.xml'...success
Checking game offsets
Loading items of usb view from usb1
Loading files containing .wbfs|.iso in usb1:/wbfs
Database file: usb1:/wiiflow/cache/lists/usb1_wbfs.db
update_games=0 update_homebrew=0 update_dml=0, update_emu=0
usb1:/wbfs
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Stop showing images
Coverflow started!
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Thread running. Stop it
Loading items of Going to show a wait message screen, delay: 15, # images: 5
channel view from NAND, which is refreshing.
NandPath = /wiiflow/nandemu
nandpath = sd:/wiiflow/nandemu/
Updating channels
Trying to open 'usb1:/wiiflow/settings/wiitdb.xml'...success
Checking game offsets
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Stop showing images
Coverflow started!
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Thread running. Stop it
Loading items of Going to show a wait message screen, delay: 15, # images: 5
emu view from usb1
Loading files containing .nes|.fds|.nsf|.unf|.nez|.unif|.zip|.7z in usb1:/fceugx/roms
Database file: usb1:/wiiflow/cache/lists/usb1_fceugx_roms.db
update_games=0 update_homebrew=0 update_dml=0, update_emu=0
usb1:/fceugx/roms
Loading files containing .smd|.gen|.zip in usb1:/genplus/roms
Database file: usb1:/wiiflow/cache/lists/usb1_genplus_roms.db
update_games=0 update_homebrew=0 update_dml=0, update_emu=0
usb1:/genplus/roms
Parsing scummvm.ini
Loading files containing .smc|.fig|.sfc|.swc|.zip|.7z in usb1:/snes9xgx/roms
Database file: usb1:/wiiflow/cache/lists/usb1_snes9xgx_roms.db
update_games=0 update_homebrew=0 update_dml=0, update_emu=0
usb1:/snes9xgx/roms
Loading files containing .agb|.gba|.bin|.elf|.mb|.dmg|.gb|.gbc|.cgb|.sgb|.zip|.7z in usb1:/vbagx/roms
Database file: usb1:/wiiflow/cache/lists/usb1_vbagx_roms.db
update_games=0 update_homebrew=0 update_dml=0, update_emu=0
usb1:/vbagx/roms
Loading files containing .n64|.v64|.z64|.zip in usb1:/wii64/roms
Database file: usb1:/wiiflow/cache/lists/usb1_wii64_roms.db
update_games=0 update_homebrew=0 update_dml=0, update_emu=0
usb1:/wii64/roms
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Stop showing images
Coverflow started!
Current Partition: 1
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Thread running. Stop it
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Launching game
Going to show a wait message screen, delay: 15, # images: 5
Game title: 1080 Snowboarding (JU) [!].z64
Filepath of homebrew: usb1:/wiiflow/plugins/wii64.dol
SHND: Stopping sound thread
SHND: Stopped sound thread