When using rdesktop with seamless RDP, every window on the remote machine should have its own local window with decorations hidden (hence 'seamless' :) )
Using rdesktop 1.5 on Hardy with seamless RDP, all the remote windows have their xserver decorations hidden correctly, and xprop shows that they have _MOTIF_WM_HINTS set for this purpose.
Here's a Temporal workaround if you're using compiz: Go to Compiz-Config Settings Manager (install it if you don't have it) and in Window Decorations replace 'any' with '!(class=SeamlessRDP)' or if you have other options you can just add '&!(class=SeamlessRDP)' at the end (everything without the quotes). Note that if you grab it by the windows border it may be a little lag before it updates the position of the window, but if you alt+grab it, everything's fine