I would need to get the project to take a look at how you have it all setup.
1) You have the Site Improvement defined in the MSI Manager
2) You have specific Layers on which these objects reside
3) You have categorized the Takeoff Layers on which they reside and you have assigned the Site Improvements to those layers in the Categorize Takeoff Layers function
4) You have reported the Takeoff and are still seeing the issue of some lines not reporting
I sounds like you have maybe 1, 2 correct but maybe 3 needs looking at to get 4 to work.
If you share the project I can take a look at it to see where this is failing, but my guess is (3) - people often categorize the Layer but forget to assign the Site Improvement - let me know if that is not the issue. The other thing I see is people think the data is on one layer but in fact it is on a different layer and that is why it doesn't report. If you assigned the layer to e.g. Unused category that may also have an effect (I have not tried that though).
Let me know if this helps
Alan