Hello all, having owned 5 octavia's I think I've finally cracked this issue.
If it's the boot seal filling with water (check by squeezing it and see if water shoots out the holes); then you need to make some on the bottom of the seal so it can drain.
I did this with a revolving leather hole punch tool; easy to find and purchase, designed for punching a hole in leather.
I chose the size that matched the exisiting holes, then popped the tool in the exisiting hole, and punched down, thus making a hole is the bottom of seal.
No more soppy boot!
I did this in line with the exisiting holes, but you could do as many as you want.
Works a treat. Good luck :)