Hi Andy,
Gearbox most likely if the clutch is OK. One point that must be followed is to use the right oil. Use only the recommended Total BV oil or another oil specifically formulated for use in Peugeot/Citroen gearboxes. Comma make one. It is a 75W/80 oil. Change it if you have any doubt. The problem may well clear up. If it remains then you most likely have a worn synchro cone.
EP90 or EP80 is commonly used but this causes a ridiculously stiff change when the 'box is cold and can damage the synchro cones through excess force being used to engage gears.
Worn synchromesh cones (especially 3rd) are common on the BE3 'box. The cone itself is made of a soft alloy and is easily damaged. This is why it is vital to use only the right oil. They are as fussy as an auto-box in this respect.
If your problem was affecting 3rd and 4th gear equally, the problem would be the other common BE3 problem of a broken baulk ring spring.
The good news is that the BE3 'box is simple and by gearbox standards, not hard to strip to replace the worn cone. The bad news is that new cones are extraordinarily expensive at £120 each
So, best advice is to get a replacement gearbox from a scrapyard.
Here is a picture of the guilty party..
I'm soon to rebuild my 205 'box and the picture is from a scrap gearbox I'm practicing on.