I'd say theres nothing wrong with the box, check your mounts, especially at the nose cone.
edit, after reading it properly is your clutch adjustment ok, free play in the pedal etc, ive only ever had reverse gear issue like you say from iffy mounts, but not from stationary, sounds like clutch adjustment to me.
Found it! (after building out the gearbox and engine). Those yellow nose cone mount.....................I will stick with original volkswagen mounts for ths time!