Hi Ali,
If you engine/clutch stack is out of alignment then it could cause the problem you have experienced.
On my N5 i am using an OS55HZ and i have used the engine spacing shims that go between the engine and mounts, to mesh the main gear to pinion i left the engine mounts loose with the engine fitted and also left the clutch stack loose then cut a strip of paper, about 10mm wide and feed it in between the pinion and main gear while pressing on the front of the clutch stach forcing it towards the main gear making it good and tight. Tighten up all the bolts on the clutch stack then while spinning the started shaft with your fingers adjust the engine alignment for a smooth feel to the start shaft and then tighen down all the engine mount frame bolts. Once this is all done remove the slip of paper and you should have a good gear mesh and a good alignment of the clutch stack and engine.
I have used the 'Paper Meshing' method for years and it works a treat for me.
Hope this helps, if you have any other questions just give us a shout.
Cheers,
Ross