I found my issue with polygon select, polygon select will only select the entities that are in view when the polygon is closed out. Therefore you need to zoom extends when closing out the polygon to make sure you get everything.
I can understand the theory behind this. There almost needs to be another tool when working with data such as cross sections that would allow you to pick a start, stop and width and select everything within this box.
You could do this via create rectangular polygon,inside boundary select, and delete or move but this would add a lot of extra steps.