I gonna guess you have two different instances of excel open and you're copying
from one to the other.
If you open both workbooks in the same instance of excel (file|open the second),
then try your copy|paste special.
Sometimes doubleclicking on a file in windows explorer will cause a new session
to be opened.
A couple of suggestions to make windows/excel behave the way I like:
Close Excel and
Windows Start Button|Run
excel /unregserver
then
Windows Start Button|Run
excel /regserver
The /unregserver & /regserver stuff resets the windows registry to excel's
factory defaults
If that doesn't work, try one more guess:
Inside excel:
Tools|Options|General|Ignore other applications (uncheck it)