I've frequently encountered problems with しまう. Usually it appears alongside て form, like 遅れてしまいました, "Unfortunately I came too late". In this case, it signals regret on the speakers behalf.
I'm having far more issues with this verb when its like here: 母からの手紙は箱の中に大切にしまってあります。
I can't even translate this sentence. I think the speaker says that his mom's letter is precious to him out of all the things in the box. But really, I don't know how to incorporate a meaningful interpretation of しまう here. Maybe like "ultimately is precious"? The て-form with ある also kind of gives me a headache. Maybe it means that the letter has reached the status "precious" and stays in that status now? It's one of the functions I learned for て form + いる. Like 窓が困っている (or ある, because its an object? I once learned that いる is for living beings and ある for objects. But I feel like いる might have been combined with non-living objects too already. My memory might deceive me on this though...^^).