2001 Clio 5th gear proble

I have replaced the gearbox in a friends 2001 Clio 1.5dci (for the 2nd time). Before fitting I checked to be sure all gears were working, they were. When fitted I checked again before connecting the selector rod, again all gears worked. I fitted the selector rod aligning it with the wear marks thinking that would be fine (worked fine with 1st replacement box). Unfortunately I seem to be lacking 5th gear now regardless of how I align selector rod. I also seem to have lost 5th gear even without selector connected. I am at a loss as to how this could have happened, any help would be gratefully accepted.