Try with only the beep3 in boot init, remove the wait & popup instructions..I don't think so, for my tests i'm running
Boot_init.txt
wait 1
popup PS3[emoji769] Pro
beep3
Autoexec.bat
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=12&pos=0x30
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=01&pos=0x377
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=01&pos=0x249
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=01&pos=0x157
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=01&pos=0x147
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=01&pos=0x40
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=01&pos=0x25E
/write.ps3/dev_hdd0/tmp/wm_config.bin&t=01&pos=0x25
wait 5
/play.ps3/dev_hdd0/PROISO/RELOADXMB.iso
wait 9
wait 9
wait 9
/mount.ps3/unmount
wait 2
/insert.ps3
Onxmb.bat
copy /dev_hdd0/game/PS34KPROX/USRDIR/toolbox/patches/game_column_fix/hfw/,/dev_blind/vsh/resource/explore/xmb/
/led.ps3mapi?color=1&mode=2
/led.ps3mapi?color=0&mode=3
Note i'm using copy because /copy.ps3 and /copy_ps3/ are not working via script, and the timings is for HEN.
EDIT:
I tried before without boot_init.txt and same issue, but with your new test build it worked