The meanings are the same, but the structure in the first is awkward.
Interested in Language
Is there difference in meaning between the sentences.
Tell me what is your comment on this issue.
Tell me what your comment is on this issue.
The first could be punctuated thus:
Tell me: what is your comment on this issue?
...but the second is much more natural.
***** NOT A TEACHER *****
You have received the answers from two teachers, and I definitely suggest that you follow their advice.
I feel, however, that you might be interested in the opinion of an old book written by a man who is still respected by many people.
His name was H.W. Fowler.
His book was published in 1926. It's entitled A DICTIONARY OF MODERN ENGLISH USAGE.
Accordng to Mr. Fowler, both sentences are grammatically correct:
Explain what are the duties.
Explain what the duties are.
According to Mr. Fowler, "it can hardly be said that one is more normal than the other."
According to Mr. Fowler, the first sentence would have this answer: These are the duties; the second sentence would have this answer: The duties are these.
P.S. If you find his explanation difficult to understand, don't feel bad. Many people joke that a person deserves a medal if s/he tries to understand much of what Mr. Fowler wrote. I notice that the above explanation is missing from the 1996 edition. I found it in the 1965 edition`on page 279 ("indirect question").
His explanation goes past me- I see no difference between the answers, and I do not know why someone would specifically seek one or the other as a response. The first sentence sounds odd to me. I wouldn't necessarily call it absolutely wrong, but I wouldn't use it.
"I notice that the above explanation is missing from the 1996 edition. I found it in the 1965 edition`on page 279 ("indirect question")."
It appears that Mr Fowler and/or his editors came to their senses.
They do move with the times, even if a little slowly and unwillingly.