I'm not exactly sure what your problem is but you might check out
Views>hide/ show edges.
Are you selecting the total shape with the solid or the hollow+ arrow or are you
using the hollow selection arrow and only selecting a portion of the shape?
are you using CS5 because i had a similar issue. selected the 2 objects but it didn't align them correctly. it was like there was an other object selected and they were not aligning to each other. still not sure what caused it but when i restarted the program and tried again it worked. i have had that happen 2 or 3 times so if someone has the answer for that one i would be interested also
There are three selection arrows, which are you using?
Also, check view>show bounding box. I personally hate bounding boxes
but most people use them.
:U Rock:In Illy Preferences, Selection & Anchor Display.
Uncheck, "Object Selection by Path Only" box