Re: Ibanez EX350
From what I can tell, the TRS tremolos used flat baseplates, and the saddles themselves were different heights to compensate for the radius of the fretboard
(This is different to say, an edge or ZR trem, where the saddles are all exacly the same but the baseplate has little shelves milled into it that raise or lower the saddles to match the radius. This way is better because it means you can buy a single replacement saddle if one breaks, and also if you take the saddles off for any reason, you don't have to remember to put them on in the right order.)
Its possible that one of your saddles is actually in the wrong place. Pull the trem from the guitar and look at it from the front (You don't really need to take the strings off for this either, but definitely slack them all off to stop the trem jumping out of the guitar once you take the springs off the back.)
What we're looking for is whether the G saddle itself, has a break point lower than the E or B strings. Check the other sadles too. If they smoothly curve, with the highest saddles in the middle and the lowest at the edges, then we've eliminated that as a possible cause. If the saddles don't do that though, then you need to take the saddles off, match them up into pairs, and then put them on in the right order, highest/thickest saddles in the middle, thinnest at the edges.
Beyond that, check nothing is fouling the saddles causing them to be raised up, check that the action at the nut is ok, and check that the saddles don't have excessive string wear on them. On softer metals, the strings can actually eat into the saddles and make the groove deep enough to cause problems. The TOM style bridges on LTD vipers are like that, mine has a big ol' low E shaped indentation on the low E saddle. You can even see the individual winds, in relief!
Beyond that, I'd say to get back to us. The good thing is, IIRC, the Gotoh GET1996t is a direct replacement for that tremolo, so if all else fails, you can go for an upgrade at a cheap price, and come away with a much better guitar. (IMO, the bridge is responsible for more of a guitars tone than anything else except electronics. You'll find the Gotoh sustains MUCH longer than a TRS too, due to the better block and materials.)