Definitly something to do with the bot, the problem the OP is describing is when he is unmounted (assuming its the same issue im having), whereas around half the mounts in game wont jump you onto the surface with water walking regardless.
Either way as this is a rather frustrating problem to have when trying to fish with a waterwalking enabled, i thought id add a log file of it happening to see if any help can be given.
I would add that this often happens when the bot goes to land, even though the water walking buff is still active, i have not been able to replicate it by clicking off the waterwalking buff after landing( in this case the bot just reaplies it and jumps back up without issue)
Whilst in most cases after 2-5 minutes of random jumping, the bot manages to finally make its way back onto the water, i am currently running without waterwalking enabled, as the slight gain in accessible pools is far outweighed by the risk and time loss of jumping randomly for minutes at a time.
This is an issue i have experienced in multiple profiles across multiple pandarian zones
I stopped the bot after about 30 seconds of the problem to help aid in finding the relevant parts in the log file.