you seem to be launching the same copy of WoW with both commands, did you do that on purpose?

[commands]
count=2
command_00=wow1
action_00=D:\WoW\1\WoW.exe
keymap_00=
region_00=region1
uname_00=1.'account1'
cpu_00=00000001
maxfps_00=30.15
excludeRR_00=0
command_01=wow2
action_01=D:\WoW\1\Wow.exe
keymap_01=
region_01=region2
uname_01=1.'account2'
cpu_01=00000002
maxfps_01=30.15
excludeRR_01=0