well, i think this is because when swimming/flying the normal jump becomes from a simple one-button-press to a movement key like the arrow keys, with the movement beeing 'up/high'.

To define space simply as an movement-key, you can do the following in hkn:
Code:
<MovementHotkey space>
   	<Sendlabel w1,w2>
   	<Key space>
(with w1,w2 the labels for your windows)
..honestly i don't know if this let you jump normal, if you have a problem with normal jumping you can ofcourse use another trigger, for a 'take-of-key' like, for example doing it with 'v' like:
Code:
<MovementHotkey v>
    	<Sendlabel w1,w2>
    	<Key space>
for more infos on MovementHotkey see: HKN: MovementHotkey

Honestly I don't know exactly if the above will fix you issue (and i can't test it at the moment), so if you could report back if it did, would be nice!