Question

I want to know what's the matter with you? 还是 Iwant to know what the matter is with you?

Answer 1

仔细找了一会儿，个人觉得这个答案应该可以满足你。
回答：《张道真英语用法》（商务印书馆）中关于matter有这样的例句：
the
matter
表示“有问题”、“有毛病”
例句：Is
anything
the
matter?
　　　What's
the
matter
with
the
machine?
　　　What's
the
matter
with
your
foot?
　　从第一句可以看出，anything是主语，the
matter
是表语，那么肯定句可以是Something
is
the
matter.
或
Nothing
is
the
matter.如果对Nothing
或
something划线提问的话，那么就是What
is
the
matter?
也就是说the
matter
是表语；what
是主语，这本身就是陈述语序了。那么在直接引语转间接引语后，She
asked
what
was
the
matter.是正确的。
　　但是，有可能这种语序读起来比较拗口，所以也会有She
asked
me
what
the
matter
was的句子出现，应该也不算错。可能2006年吧，重庆市中考题中就出现了what
the
matter
was的正确选项，所以这种说法应该是已经被大家所接受了吧。
但从严格的语法意义上来讲，She
asked
me
what
was
the
matter
是正确的。
引用一位美国老师的话，可能从日常用法上说明一下：
　　Could
you
tell
me
what
the
matter
was?
is
the
more
normal
version,
but
I
can't
really
say
why:
it's
mainly
a
question
of
rhythm,
I
think:
it
sounds
a
little
better.

Answer 2

I
want
to
know
what's
the
matter
with
you?我想知道你怎么啦?
Iwant
to
know
what
the
matter
is
with
you?我想知道发生了什么事吗?
看你表达什么意思的，但一般我们用的都是第一个。