Unless you buy matched pacs, there will always be differences between cells in a pack. If you are using both pacs such that mah consumed should be the same, then the diff would suggest you have a weak cell or one getting weak in the pack taking less.

When you charge this pac, see if you feel a cell thats hotter than the other cells. This would be the one thats getting weak (internal cell resistance is gone up and generates more heat when charged).