That is why pharmaceuticals typically contain binders, excipients, release agents, etc. If such additives are suitable for your application, then you might want to consider them.
I was facing similar problems a few years back. The only probable, error free and less time consuming solution is making your own die set. Find a good mechanical engineer, design a die with lesser cylindrical length. The one i used was only an inch in height. But the die set has to be made of high carbon steel plated with nickel. It really helped me in preparing my polymer pellets
Ratnakar has given some solution. The dye quality must be good. Also, conducting polymer can absorb moisture, have lot of secondary interaction. Dry the sample and try to pelletize in dehumidified room.