There’s your answer right there and it was what I betting on. There is a well known issue when one has two objects on a plate. The speed of the transition from one model to another influences each other and his very apparent in the scenario you described.
You actually have two problems. The first is the issue with filament flow influenced by two models on the same plate of different heights. The second issue is that it’s unclear whether or not your filament is properly calibrated. Fix issue one before moving onto issue two. You may not need to readdress the calibration.
The fix “Print by Object”
You want to turn on “Print by Object” under the Global Process Menu under “Others”
What this will force the slicer to do is complete one print before moving on to the next model. There is a throughput cost here. Because the slicer knows there will be a completed print on the plate before starting the next model, a safety measure is put in place that restricts how close two models can be to each other on the plate. This ensures enough clearance for the print head to avoid interfering with the model already standing on the plate. This may prevent all of your models from fitting onto the same plate, necessitating more than one print.
Here’s what that looks like when Print by Object is turned on and the two objects are too close together. I will use two cylinders of approximately the same size as your example to illustrate what you will run into.
How to arrange on the build plate automatically
Just click on autoarrange.
If there is enough room, the slicer software rearrange as many of the objects onto the plate as possible and move the objects that don’t fit off the plate.
If you do not have additional plates available, it will simply move them to the “outside” category.
Here’s are two tricks to increase model density on the plate.
Trick #1 – Manually manipulate print sequence and location.
The slicer’s software will do a very coarse estimate of where prints can fit using autoarrange. What I prefer to do is to micro-manage that process by changing the sequence in which the models print and then moving the taller models to the front of the plate and the shorter ones to the back.
Here’s how that works. In example one, the cylinders all collide and the slicer won’t let you slice.
Manually drag the models into the desired order in the plate window, with the first model listed on top and the last model on the bottom. This will ensure that once model #1 is completely printed, it will be out of the way of the other models.
BTW: A by-product of this is that you can pause the printer and snap off the completed model without waiting for the entire print to complete.
Trick #2 – Create an assembly of two smaller models.
If you merge two models together as an assembly, the slicer will be tricked into treating the combined model into one. Note that if they are different heights, you’ll get the same lines. But if they are the same, then combined them.
Here’s how that looks.
After assembly, the slicer treats the combined models as one and allowing for closer spacing.
For a better explanation of why this phenomena happens, view this video. This is where I got my answer from when I first ran into this issue.