Our Chippy was 'not quite right' for a while after we fitted a new engine last year. It was much improved by applying the 'plug mod' which enables us to use more up to date plugs in the engine - but it still 'missed' occasionaly (notably on take off from G-VFWE this year, cuasing a land- back). Another symtom was 'juddering' of the engine when reducing power. It ran fine at high power, missed and juddered during the power reduction, then ran fine at the new power setting.
The engineers couldn't fathom it. The fault eventually went away when a mag was changed at a 50 hour check - becuase of rough running.
Fingers crossed, it seems OK now.
SSD