Package: x2goclient (win64)
Version: 4.0.5.0 (Qt 4.8.6)

1. start a server using windowed geometry 
  - 1440x900, RHEL5 (but any non-fullscreen res reproduces)
2. maximize window
3. start incisive enterprise simulator program (cadence IES tool)

Notes:

omitting the maximize (step 2) yields normal results
x2goclient on linux does not suffer from this issue
vnc both windows/linux does not suffer from this issue 
  - (no way to rescale geometry after server is started)

The rest of the windows spawned by IES all suffer from this...

I haven't observed this with other programs, so I'm attaching the strace for reference.