@Marko G
Each of the problems you mentioned has to do with the placement of your Queues and your network of "Next Look For Work" connections.
The thing with AGVs when using the AGV process flow is that they don't know how to get to the items that are available for pickup unless there are "Next Look For Work" connections or "Look For Work" connections leading to them.
AGVs follow these steps when collecting items:
1. They follow the "Next Look For Work" connections until they find an item to pick up. If there are no "Next Look For Work" or "Look For Work" connections to a control point, it won't go there to pick up items.
2. They load the item.
3. They travel directly to the destination of that item (regardless of where "Next Look For Work" connections lead).
4. They unload the item.
5. They follow the "Next Look For Work" connection from their current Control Point and continue looking for work.
Here are my answers to your questions:
1. Following the steps I described above, the AGV loads at D7 and travels to R7 using the shortest path possible, then unloads the item. Then it follows the "Next Look For Work" connection to continue searching for work. Referring to the image below, it follows the "Next Look For Work" connections until it travels back to the base floor.

It continues traveling like this until it finds work at D2. It then travels directly to the destination for D2, which is R2. From R2, the "Next Look For Work" connections lead back to the base floor, which is why it returns to the base floor even when there is no work available there.
You can try fixing this problem by reorganizing where your source and destination queues are, by changing the AGV paths, or by changing the network of "Next Look For Work" connections. For example, you could move R2 next to R4 (I don't know if that is possible for you), so that after delivering the item from D2 to R2, the "Next Look For Work" connections would lead it to the other queues with items (D8, D11, etc.).
The difficult part about fixing the inefficiency in your model is that everything is so spread out, it's hard to check every queue without wasting some time. You can play around with it and see what makes it more efficient.
2. Yes, that would reduce travel time. If you can, I would recommend removing most of the path above R4 and then moving the floor-to-floor connection, the elevator entrance and the elevator redirect down.
3. I'm not sure I understand this question. Are you asking why the AGV doesn't travel directly from R7 to D8? If so, refer to my answer to question 1.
Hope this helps!