tenses

Fine - apart from the comma in b, which should be:

'I'm so glad! What a relief. The design of the control system has been troubling me, and sometimes when I look at the equations I wonder why the second variable is a function of y2.'

badegine,

What do you think of the following?

'I'm so glad! What a relief. The design of the control system had been troubling me, and sometimes when I looked at the equations I wondered why the second variable was function of y2.'

What do you feel when you hear it in the context mentioned before? Try to avoid using grammatical terms in your explaination. I would like to know how you feel as a native speaker (I think you're, right?).

Also, which tense would you prefer? I'm trying to see whether it's a matter of preference.

Thanks in advance!

Hi Anon, I don't understand the need for a 'clue phrase' phrase explanation you provided. You mean you don't use the past perfect continous tense without an additional phrase like what you suggested in your  example but you have no problem with the present perfect continous standing alone? Interesting- something new to me.