Syntax

a. Perhaps you can tell me when you see me again? This sentence doesn't make much sense. Basically it means you're hiding or have disappeared, and you're asking the person when you become visible again.

b. Perhaps you can tell me when you will see me again? This is better. It's asking when the person would like to see you again.

a. Perhaps you can tell me, when you see me again?
This is asking that maybe, when "you" see "me" again, you can tell me (about something). Employing a comma between "me" and "when" helps to clarify the question.

You can rearrange the clauses to read, "when you see me again, perhaps you can tell me?"
b. Perhaps you can tell me when you will see me again?
This is asking that maybe "you" can tell "me" when, i.e. at what time, date, etc., "you" will see "me" again.