这是宾语从句,但正常词序应该是：I don't know what the matter is with you.（the matter 【主语】+is with you【系表结构】）还有 I don't know which the way to +地名+is （the way to +地名【主语】+is系动词）
宾语从句语序决不能是疑问语序.
例句：I don't know what I can do
I 主语
can do 谓语