As nick said it could be as a result of a drainage problem, but I have never had the boot filling up problem . But before any further repairs there will be a hose session to see if anything appears from above ! Salvation I hope !
The area is a real rust trap and any condensation has no where to go , but gravitate to the seems which being inside the boxes cannot be sealed and again looking there is not an awful lot of paint in the box areas. All I can do once new bits of steel are knocked up and welded in is to liberally squirt the area with waxoyl or similar from the 2 local access holes, off course I hope that I can seal the joints externally to prevent water ingress from outside .

 

Emptied a 600ml tin of a WD type of water repellent in the sills after Hammerite underbody black sealant on the underside outers of the car,<with waxoyl>5 grommets a side,will do the rear as forgot wheel arch ones.
My car stinks of WD now and is making me feel sick,
hope it goes away soon

 

Well Noodels I can understand where your coming from regarding solvents , I have made comment before about the toxic nature of Waxoyl , and that the stuff contains white spirit and that is also the recommendation for thinner when spraying the stuff into box sections . It gave me horrendous headache when using it until I realised and started using a proper respirator , so beware.

Any way I have now fabricated a small patch panel and mig welded it in , bit tricky as the Honda steel that the cills are made of is something like 0.75mm thick so very easy to blow ruddy great holes in. So with mig welder set on mins ( think I would have preferred oxy cet from what I can recall from my college days , but any way it's welded in albeit with a few little hols showing . These will get filled when I fill the whole area with water proof filler prior to sanding and forming the best shape I can to match the line of the original panel. It doesent seem to bad to me even as it stands .

I often wonder about welding in patch panels etc especially when into box sections , I used 1mm galv steel plate as that's what I had so there is protection to some extent inside on that but not where the OEM paint gets burnt ect . So you can see I came up with a cunning plan . I took the spray cap of a WD40 can and the little red pipe and stuck those on a can of Zinc primer , and stuck that pipe up the box section drains , inspection holes and through a couple of my weld holes and liberally sprayed until it appeared through the joints and seams of my repairs and every where else . I tried and hopfully this will help keep the
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