Stopping at fences is a good thing?

If you read the title to this post you're probably just about as confused as I was during my jumping lesson last night. Fortunately, Alexis is very good at explaining and I ended up understanding his point.
We started our lesson last night working on keeping Gatsby straight; he tends to pop his outside shoulder out a bit. We worked at the trot and canter on a circle with me focusing on my outside aids as well as keeping him forward, relaxed, and stretchy. Gatsby is a very smart horse and he loves to please so he caught on very quickly and we moved on to trotting some low fences. We wanted to keep him in that same relaxed mind frame that we got him in last week, once again my horse is very smart and he knew right away what I was asking from him. After popping over a cross-rail a few times we moved on to a small vertical on a diagonal. I'm sitting there thinking how great my horse is for staying so relaxed and responsive when all of a sudden SUPRISE! Gatsby stops. My horse rarely stops so I am a little surprised but I rein back and trot him over it...a little messy but he goes over fine.
After a few more rounds of that we moved on to the tough part. Alexis had me ride a line from a vertical to an oxer, both approx. 3 feet. Gatsby jumped the verticle smoothly, I half-halted, sat back and stayed quite to the oxer (we're working on me not doing anything on the approach and him staying relaxed and figuring it out on his own). BAM! He stops again! I have no idea what is going on at this point and I am racking my brain trying to figure out why my horse is all of a sudden refusing simple, low fences. That's when Alexis says "That's exactly what I wanted to happen." What?!?!?! After a little explanation I understood his point; Gats is used to me riding him to fences with a strong leg and a short rein. He usually rushes to fences and has a very short and elevated stride and it is necessary for me to pick up a strong contact and really guide him over the jump. When we took away all of this "discussion" in the approach and had him come to the fence at a nice relaxed, reaching canter with loose reins, he didn't know what to do. After a few more stops and some very ugly fences Gatsby figured it all out and hopped over the oxer without a second thought.
This whole exercise really got me thinking about how I have been riding him in the past and why we started having problems on course all of a sudden. That's when what Alexis said about him not knowing what to do without me really made sense. I've been letting him do things his own way and accommodating his bad habits by overriding instead of just training him to things the right way. I think that this new style will actually help us develop faster once we're both more used to it. I would have been terrified to ride him around a Prelim course the way we were going before but if I can get him to stay calm and figuring things out for himself, I think I will be much more confident.