Does a box come up that says 'delete isolated verticles'? and if so do you click 'yes'? If you do, then you are deteting vertices whenever faces get removed or moved around etc... Just click no next time
If the answer to both the above questions was no, then sorry I cant help :S
if you are in editable mesh, you can only see the vertices for THAT object. To see the vertices for the object you attached, go to select by name at the top, and select the object you attached.
