I have a similar problem on my 82,000 mile 2002 ST1300A. I have replaced the O ring seal and still have the leak but notice that the o ring is not a good snug fit in the grooe of the water pump cover. This makes it easy for the O ring to displace during refitting of the cover. Today I enquired of David Silver U.K as to whether the early ST1300 O ring has a different part number and was quoted a different one to that ordered/ I recently replaced. The early part number is 19226 MCS 000 compared to the one I fitted earlier of 19226MCSA10 which looked the same as the 1st I replaced which was not a good fit either. That probably wasn't the original as the bike has had a clutch change in prior ownership. Any thoughts please?
If the cover is not properly torqued down, it will cause warping of that cover, thus a leak!
If you have torqued it down to proper values, I would check the cover on a really flat surface, and also check the main engine front cover, make sure it is clean and flat.
Always replace that pump cover o-ring type gasket when it's been apart.