I too had water collecting in the spare wheel well of my 3.2 saloon. The boot lip seal seemed fine, but I changed it for a known good one off another car with a dry boot, without any noteable improvement. With further delving, I did notice that, as Carfix has said, there was a minute gap between the spot welded seam in the nearside boot lip aperture, directly below the rear screen rubber moulding. Shining a inspection lamp inside the boot in that area helped to pinpoint it as you could see the light between the two panels. Rather than use seam sealer, which would have involved a bit of paint touching up, I forced some DumDum in with my finger from both sides. This seemed to have cured it, and the beauty of DumDum is that any excess can be removed with White Spirit, leaving just the correct amount of sealant in the affected seam which skins over but remains flexible, without any overlapping as with brushable seam sealer. It's barely visible, and doesn't look out of place, and requires no touching in with paint.
Incidentally, if your boot lid sits well between the rear wings, without being proud, don't be tempted to try adjusting the hinges.....before I found the gap in the above seam, I tried adjusting the hinges as mine was marginally proud on the unaffected side, but what a mistake that was... any adjustment I attempted seemed to have the opposite affect, and trying to get to sit as it should once the allen key bolts had been slackened was a nightmare. I did get it right in the end, but not without a lot of cursing and swearing......