endAre you sure that the affected ports are connected to a computer with a Gigabit ethernet socket? If it's a (slightly) older computer with a 10 or 100 Mbps ethernet port then the link will only work at that speed. Cat5e will run Gigabit anyway, over short distances.
If it is the cable that's restricting the speed then check for continuity on all 4 pairs. 10 and 100 Mbps only use 2 pairs, but Gigabit needs all 4, so if there's a fault on a wire that might cause a link to downgrade. It might be as simple as one wire not punched down properly or snapped off as you put the faceplate on the back box.
It looks neater with minitrunking if you run the trunking further than where the cable goes into the wall, run the cables into the wall through a hole in the back of the tunking leaving the sides and front continuous and then put a stop end on the end of the trunking.
If it is the cable that's restricting the speed then check for continuity on all 4 pairs. 10 and 100 Mbps only use 2 pairs, but Gigabit needs all 4, so if there's a fault on a wire that might cause a link to downgrade. It might be as simple as one wire not punched down properly or snapped off as you put the faceplate on the back box.
It looks neater with minitrunking if you run the trunking further than where the cable goes into the wall, run the cables into the wall through a hole in the back of the tunking leaving the sides and front continuous and then put a stop end on the end of the trunking.