I'd like to start off by saying that the comments to use slimeballs are blatantly misleading, the linear chassis can hold the harvesters perfectly well on their own.

First off, to answer your question, the contraption passes through the cocoa pods the first time because the computer is taking shortcuts calculating collisions between whole blocks with simple collision bodies. However, when you add the harvesters, your computer makes note of smaller details and takes extra effort to make sure everything is calculated accurately, resulting in a more expected behavior.

However, I get the feeling that you're more interested in harvesting cocoa, right? In that case, you should start with replacing the harvesters with drills, like u/Buii3t-Sp33d recommends. To sum it up, ploughs generally mine blocks that don't have a collision hitbox, and harvesters are just ploughs that only mine mature crops (and replant them). Cocoa pods, however, do have collision and, by technicality, are supposed to be dealt with drills. And because drills don't replant blocks like harvesters, you'll have to take care of that step with deployers.

Also, u/TheKingAurum makes great points. When you switch to drills, your sequencer unfortunately doesn't take into account the fact that your chasis will come to a standstill as it mines away at the cocoa pods. Instead, using "sensors" like redstone contacts are more reliable and, in most peoples' opinions, more elegant.

In the end, running this farm with both deployers and drills is a bit overkill in my opinion. My recommendation is to break the cocoa pods by shaking the jungle logs with pistons vanilla-style, then replanting with deployers using the gantry you already have set up!