Because I was curious about the literal meaning of this phrase, I looked it up on Wiktionary. "cónaí" apparently means something like "home," "dwelling," or "resting place." So "i gcónaí," which can be interpreted as "always," "yet/still," or "ever" is perhaps somehow connected to the idea of being at a resting place, or figuratively remaining/resting in some state (e.g. trouble, Paul's case). Interesting.
Because you can't make a question in Irish using the same words as the statement. The question "Is Paul always in trouble" would be "An bhfuil Pól i gcónaí i dtrioblóid?", using some material (an bhfuil) that hasn't been covered yet.
The sentence Tá Pól i gcónaí i dtrioblóid can only be the statement that he is in trouble.