1-Then you need to find out what is wrong with it.
2-You then need to find out what is wrong with it.
3-You need to find out then what is wrong with it.
Which of these sentences can be used if the intended meaning is:
a-As a consequence of what has been said, one would say that you need to find out what is wrong with it.
Jack says: My computer isn't working properly.
And Jane replies: If that is so, then you need to find out what is wrong with it.
In other words, "then" is not supposed to have a temporal meaning here.
I think in "2", "then" could only have a temporal meaning and therefore "2" would not work in this context.
"3" sounds informal to me.
Given the intended meaning, 1 is the most common by a very wide margin.
As you say, 2 would likely be used if then were temporal. But given your intended meaning, a person hearing 2 could easily rule out the temporal meaning.
All three seem intelligible, but 2 and 3 would rarely be heard in actual usage.