I see have you by chance mapped the arrow keys for movement or something else? There you have your problem. For some strange reason you can't map all the keys from within the game. Hehe by looking at the binds.cfg I discovered as I am writing this that you can climb with the mouse buttons! 1 MB Indy climbs up, 2 MB Indy climbs down and if you do not like that you can alter it in the binds.cfg which is located in your IJET directory under Gamedata\indy. So back to your problem I guess you have mapped the arrow keys for movement and by that double mapped the up and down keys that are "hard" mapped to climb up and down. So now you have two choices either change your movement keys to another location or edit the binds.cfg If you want to do the latter look for this 2 strings:
setbind 0 COMMAND_CLIMB_UP
setbind 0 COMMAND_CLIMB_DOWN
change the keys from key_up and key_down and everything should work for you now.
The heart of Kouru Watu will be yours