Even the simplest Flex project using the normal s:RemoteObject syntax moans it can't resolve RemoteObject. The rpc.swc is correctly listed in the build options. You can replicate this by creating a new Flex project and add
<s:RemoteObject>
</s:RemoteObject>
in the fx:Declarations block.
FDT5 on Linux, Eclipse 3.5 though it also happens on my licenced FDT3.5. Works fine in Flex Builder.
Screen shot : http://dl.dropbox.com/u/568024/fdt5-remoteobject.png