The wagon tailgates and doors should all seal without issues if the rubbers are newish, un-damaged and fitted correctly.
Check for panel alignment before you do anything though, the rubbers can't seal if the gaps are too wide.
So the approach would be:
1. Check/adjust panel gaps
2. Check rubber condition
3. Replace any suspect rubbers
4. Refit rubbers as per factory
There are some other tricks, like putting Sikaflex behind the rubbers and then lightly closing the doors. This will make the rubbers sit out a bit further and should help them seal better - but its a balance between seal pressure and the door/tailgate shutting correctly.
Contrary to lots of stuff written up here Rare Spares rubbers do fit quite easily and will seal perfectly. So maybe you need to look at a new rubber kit, especially if you are using it daily. They'll rust very quickly if they are filling up with water.
http://www.rarespares.net.au If you don't have much experience with this stuff then join your local FE FC club, these blokes will always be willing to assist.
Hope some of the above helps.