If there is movement in the base when weight goes on it, with respect to the walls, you will struggle to solve this problem. Even the best silicone sealants just won't be elastic enough to stretch.
Establish if this is the cause (may demand some crouching in the shower - or put small wedges of card in with you stood in there, get out and see whether it is now trapped because the narrowing the gap).
If this is the case, you only way I have managed to sort it (apart from pulling the tray out) is to load the tray with a lot of weight, to force open the gap. I did it with 4 bags of cement. You could use bricks - but you need about 100Kg in there. This sounds extreme, but it similar to the weight of a heavy person standing in there. Then you can refill with new silicone (clean out all the old stuuf first obviously.
When the silicone is set, remove the weight.
What happens is that the silicone is put under compression when not being used, but sits normally when someone has a shower. You are currently putting the silicone under tension. Hope this cumbersome explanation is understandable.