The caulking seals timber joins. It`s likely leaking, failing at the edges. You could dig it out and replace with fresh polyurethane caulk, like Sikaflex 291. Then redo the varnish, covering the caulk as well. Tape the edges of the area to be filled before caulking.
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BruceK
2005 Integrity 386 "Sojourn"
Sydney Australia
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