I did some quick searching since I didn't know the process of removing the pulp and inner membrane and from what I found my guess would be that it could an pH issue causing fermentation trouble. From the info below I am assuming the wet method is used to produce the material you are trying to ferment.
Do you have a way to test acid and or pH?
Quality coffees must be picked by hand, a process that takes from three to four visits per tree each year. This is because coffee cherries do not ripen at the same time. A branch of a tree might simultaneously bear blossoms, green fruit, and ripe cherries. A good picker can pick about 200 pounds of coffee cherries in one day. This equals about 50 pounds of green coffee beans or 39 pounds of roasted coffee. Once the coffee cherries have been picked, the beans must be removed from them. Three methods may be used in the extraction process:
<LI ="texto">The Wet Method or Washed Coffee - This is used in regions where there is a plentiful supply of fresh water. A machine first strips away the outer layers of skin and fruity pulp. The beans, still enclosed in a sticky inner pulp and parchment wrapper, are soaked for 24 to 72 hours in fermentation tanks. This loosens the remaining pulp through a series of enzymatic reactions, which is then washed away. Time in the fermentation tanks is critical as too much or too little time will harm the beans. These coffees will generally have a higher acidity and cleaner flavors than their dry cousins.
<LI ="texto">The Dry or Natural Method - The cherries are allowed to dry on the tree or are laid out to dry in the sun for three to four weeks. When the pulp has dried, a hulling machine strips away the outer skin and pulp. Although the beans are not always consistent in quality, the acidity of the beans is reduced and the body and earthy flavor is increased. Producing high quality coffee with the dry method is challenging because the beans are exposed to climatic conditions during the drying process. Some of the dry method coffees are Sumatra, Ethiopia Harrar, and Yemen.
<LI ="texto">Semi-washed method - In Sulawesi, the coffee cherries are washed and sorted as in the washed method, but are not placed in fermentation tanks. Instead they are set out to dry. Sulawesi coffees are a bit more cleaner and smoother than their Sumatra cousins.
After the wet or dry process, a mill removes any remaining parchment and the silverskin - a thin covering that clings to the bean. </LI>[/list]Edited by: masta