Caulk Underneath Shower Frame?

I have a shower stall with two slider doors. I had to disassemble the frame recently. When it was professionally installed a number of years ago, the vertical frame members were caulked with clear silicone on both the inside and outside edges. The bottom frame member however was only caulked on the outside. When disassembled I found a lot of mildew underneath. I can understand why you would not caulk the inside edge of the bottom frame because it could block the weep holes, but why not underneath?
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The problem I have seen is that the mildew grows on the backside of the caulk. That's what it does on ours. I can spray bleach on the exposed caulk but that does nothing. I have to remove the clear caulk and replace it. You just can't keep the water out of the frame channels. I think the frameless ones are probably the best. Just glass glued together with clear caulk. Like an aquarium. Or maybe if you used framing that was white and then you could use white caulk. Generally it sucks. Our master shower gets used everyday and it seems like it's not very long after I work on it that mildew is starting to appear in the caulk again. Even when I use the good caulk that supposedly is mildew resistant. I will avoid these framed enclosures in the future.
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