Being married and a father of 5, I can sympathize with Civil 3D gravity pipe networks, they are always being pushed around. Many differnet things are telling pipes and structure what to do, just like in my life. Rule Sets, Structure Constraints, Alignment referneces, and Surface references can all impact the way these parts get drawn.
Rule Sets can of course affect where the pipe enters and exits a structure, thus having a ripple effect on the structure model itself. Alignment and Surface references can affect things like Rim Elevation and sometimes have a ripple effect on the pipes. Another thing that can easily be forgotten is the Structure constraints. These can have a ripple effect back to everything else. The better you understand what effects what, the easier it is to tweak to get the desired results.
Both the Rule Sets and references are pretty well documented and understood, so let's focus on the Structure constraints. For example, lets take the stock Concentric Cylindrical Structure and determine why we cannot "shrink" this part to less than 6" (72") in height with a pipe size of 18" connecting. Let's take "Concentric Structure 48 dia 24 frame 36 cone 8 wall 10 floor" and pick it apart.
You will need to take into account all of the constraints set in Part Builder to full understand what is holding us back and also give us clues as to make adjustments for it to fit. Looking at the parameters we have:
Floor Thickness 10.000"
Frame Height 8.000"
Barrel Pipe Clearance 6.000"
Cone Height 36.000"
Now taking that information into a formula that determines the drawn structures height we take:
Pipe Diameter 18"
+ Pipe wall thinkness 4"
+ Cone Height 36"
+ Frame Height 8"
+ Barrel Pipe Clearance 6"
18+4+36+8+6 = 72"
Given these parameters it is not physically possible to get a shorter structure in and maintain the 18" connecting pipe. If shorter structure is required, you can easily modify the Cone Height to something like 24". This will give a full 12" of play in placing your structure.
This is just a quick example of what may be controlling the sizes. Be sure to keep the constraints as well as rules and references in mind when designing your networks. Hope this helps!