A tabela de cores é armazenada no registro HKEY_CURRENT_USER\Console
Salve e execute isso como invert.reg
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Console]
"ColorTable00"=dword:00ffffff
"ColorTable01"=dword:007fffff
"ColorTable02"=dword:00ff7fff
"ColorTable03"=dword:007f7fff
"ColorTable04"=dword:00ffff7f
"ColorTable05"=dword:007fff7f
"ColorTable06"=dword:00ff7f7f
"ColorTable07"=dword:003f3f3f
"ColorTable08"=dword:007f7f7f
"ColorTable09"=dword:0000ffff
"ColorTable10"=dword:00ff00ff
"ColorTable11"=dword:000000ff
"ColorTable12"=dword:00ffff00
"ColorTable13"=dword:0000ff00
"ColorTable14"=dword:00ff0000
"ColorTable15"=dword:00000000
E o seguinte é o default.reg
no caso de você querer voltar
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Console]
"ColorTable00"=dword:00000000
"ColorTable01"=dword:00800000
"ColorTable02"=dword:00008000
"ColorTable03"=dword:00808000
"ColorTable04"=dword:00000080
"ColorTable05"=dword:00800080
"ColorTable06"=dword:00008080
"ColorTable07"=dword:00c0c0c0
"ColorTable08"=dword:00808080
"ColorTable09"=dword:00ff0000
"ColorTable10"=dword:0000ff00
"ColorTable11"=dword:00ffff00
"ColorTable12"=dword:000000ff
"ColorTable13"=dword:00ff00ff
"ColorTable14"=dword:0000ffff
"ColorTable15"=dword:00ffffff