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Hello, I seem to be losing a lot of money on really great starting hands that go to chit when the flop comes out. IE. $400Pl room $2 and $4 blinds.

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Are you only playing these hands? If so, you're probably playing too tight and you're opponents are going to figure it out. Why do you think A-A-2-5 double suited is so good? You are not wrong, but if you want to play these hands profitably, you need to understand what you are playing.

You are playing for another Ace, two flushes, the wheel, and the low. These are low probability hands to hit, with the exception of the low. You should keep in mind that you're aces are probably dead because of the calls to your raise.

With the starting hand you use, you either want lots of callers in case your rare cards hit, or very few so your aces can stand on their own, but the latter is much harder to play because A-A overpair is not good in Omaha/8 nearly as often as it is hold'em. In other words, you are guaranteeing yourself a tough decision, and you need to have a feel for the game and your opponents before you place yourself in this position.

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The flop comes JJ3 rainbow. If I check here I give the green light for any of the other 2 people to try and steal.

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So don't give them a chance to steal. Raise! This is not a great flop but its not bad either. You have aces up, with no low on the board. You have a fair chance of scooping the pot.

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If I bet and get called, I feel that they might have the Jack.

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Precisely, that's information you want to have. With the flop, you are worried about two hands. Jxxx and 33xx. If you want to play your A-A well, you need to know how likely it is one of your opponents has these hands. Sit down and do the math. You should find that with two opponents, there is about a 33% chance one of them has a J. (Add in the 3-3 and your odds of having the best hand drop further.) Now take these odds and apply them to your opponents. This is why the way you played your A-A is so hard. BTW, the basic odds of having a J or a 3-3 is just the start of your thinking process. You raised, so would your opponents call you with 33xx? Jxxx?

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This is just an example, but it is frustrating when other players play these type hands really fast and hard and win the whole pot with a pair of aces.

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The most dangerous thing in poker is letting your play be affected by what you see on the table. Pick a strategy and stick with it. (If it doesn't work then fine tune it, but only after refelction.) The people you see winning with A-A have most likley decided they are going to bet the pot for at least two rounds before the flop. If you are not willing to play this aggressively, then you can't get yourself into this situation with the pre-flop raise.