This result is due the direction that the sheet gets filled. I'm guessing you selected Y direction. This results in Part 4, in your case, getting stuck at the odd location because it can get lower. I have found that this slight fit is due to the True Shape nesting. We do have an option for Cut Line nesting that doesn't try to do this type of fit. I will turn it on in the next version.
The sheet filling starts at the Nesting Corner. Nesting Corner is the corner on the sheet from where the nesting process begins. ShopBot Link allows nesting from four corners: Lower Left, Lower Right, Upper Left, and Upper Right.
Nesting Direction is the direction in which the sheet gets filled (and not in which the parts get nested). Nesting can be done either in X direction or Y direction.
If the nesting direction is X, then parts will get nested along Y and if the nesting direction is Y, then parts will get nested along X.
The following figure illustrates how the nesting pattern differs upon the combination of nesting corner and nesting direction.
Here is an illustration for the nesting process.

- Nesting Direction Description.JPG (40.2 KiB) Viewed 29860 times