Maybe you are copying to the wrong clipboard.
X11 applications currently use two of the three possible clipboard buffers, one for the select and paste with middle mouse button and one for "real" clipboard (similar to the one use in Windows)
If your application is for example only copying to the first buffer, a paste from the second buffer doesn't necessarily see it.
Clipboard applications like xclipboard or KDE's klipper can be used to keep those buffers in sync on the users demand, but usually this isn't necessary if applications access the two buffers as recommended here:
http://freedesktop.org/wiki/Standards_2fclipboards_2dspec
Cheers,
_