Hi Ham88,
Indeed, it's a strange behavior. Calibre usually gives very good results (in lrf conversion which is the format I use). Maybe your pdf source is not a "normal" text based file.
My only suggestion (I'm pretty sure other expereienced members will give you more) would be to give another try with the following online converter:
http://www.lib2go.com/
I have tested for lrfs and it gives fair results.
Good luck!