Yeah I took a look at that bit of code. From what I can see though it simply checks if the bot is about to go down a ladder and slows down to ensure it doesn't go flying off the edge.
I added a bit of code which draws the direction in which the bot wants to move if the movetype == MOVETYPE_FLY. This is the result:
The red line is the bot's path, the yellow line is the direction the bot wants to move. The bot is looking at the top of the ladder (which is invisible, but it definitely works as I can climb it fine) and is trying to move forward (as shown by the yellow line). I have commented out all of the movement code so that all the bot is trying to do is move towards the next point in the path (so no trying to check if the point is reachable, no pushing away from walls etc.)
There must be something missing because the bot is frozen at the foot of the ladder, no movement at all. It's as if the moment the movetype becomes MOVETYPE_FLY, the bot is completely unable to move. It can't even move sideways.