Without XFIXES the client calls GetSelectionOwner() before every paste operation and therefor always knows the current selection owner.
With XFIXES some clients rely solely on the XFixesSelectSelectionInput/XFixesSelectionNotify mechanism. But they never receive any notifications because the nxagent does not register at the real X server to receive those notifications itself and so never gets anything to forward to the clients. A client assuming it will get informed about owner changes skips the GetSelectionOwner() call. So it never knows that the selection owner has changed and refers to what it thinks the current owner is (itself).
Attached is a fix for this bug. nxagent calls XFixesSelectSelectionInput for all its selections (t.i. CLIPBOARD and PRIMARY, _not_ SECONDARY) now. It (still) does not check the return code but the original code registering only CLIPBOARD did neither...
This is a complete patch generated by git format-patch after using (d)quilt as documented in the wiki.
As I did not find any hints of what patch number to choose I took 207 to put it as close as possible to other clipboard related patches. Feel free to change that...
Uli