Allison C30 Surge
Could be the things as described already but also have a look at the engine against a power check chart. If it is making a lot of power and is really strong could be a turbine nozzle problem as Tynecastle says i.e. too tight in area hence the cough. Have seen this in an AS350 Soloy conversion - engine had all the power in the world but would snort off ground idle, nozzles changed, no more snorting and no more power as well - long faces all round. Only one of many things of course. Your Allison shop should know what's wrong with it and of course being a twin that's what the other engine is really for, a supply of alternative components.
Aside from that you say you have had this problem for 18 months. What happens when the other one stops and you have to rely on this engine??????