The slides in our HT26.5RKS are exactly like yours and your description of the operation is also the same as ours. During our PDI, I asked the service tech if the ratchet noise was normal and he said that it was. So when we extend and retract the large slide we keep our finger on the button until we hear the ratchet noise (but only let it click once or twice before releasing the button).
One thing the service tech told us about the large slide was that you must always completely extend or completely retract the slide. In other words if for some reason you stop extending the slide part way, don't reverse the operation but rather go ahead and extend it all the way out before bringing it back in.
He also told us that the bedroom slide (different system) must always be extended or retracted completely without interruption. If not, you may need to reset the slide motor (in the front basement compartment).
The one thing you mentioned in your OP about the slide possibly being out of square. Our slides fit perfectly against the gaskets so if yours don't, I would suggest taking it back to the dealer for service while it's still under warranty. You certainly don't want any water infiltration while cruising down the road. You can also call Jayco customer service for their input on this.
Good luck and happy travels