I use my hydra grid in a pattern illustrated below:
Basically a central area with for corner areas.
What happens is that any window in the central area ALSO becomes split between the upper and lower halves as if the boundaries go through the central area which they clearly do not in the hydragrid configuration. If I remove the left central devide then the problem goes away, so that may help narrow down the cause, but I would like to know if this is a known issue, and if there is a fix or workaround for this issue.
I did find a workaround on my own by simply moving the side partitions slightly out of alignment. This allows the central area to be used as intended.