need help on tracking report folder naming
 

Hi gang,
I am in awe of all the knowledge on this board. I feel like such an infant. Anyway even though I have tracking with my server I've signed up with hitslink for awhile to compare. but one thing is confusing me on my results. For tracking my inner pages I am getting things like .../.../homes/0_100.htm and .../farms/farms.htm when my normal path is /farms/farms.htm.
I assume I have some sort of path screwed up on a page to get both results yet I can't find it. Will this effect the searchengines from indexing my inner pages? Thanks