I recently had this problem because the LBS misinformed me. I was running Sram X3 trigger shifters with Shimano altus derailleurs. Certain models of Sram shifters are compatible with Shimano der's. While some Sram shifters are only compatible with Sram der's. Its the cassettes/freewheels that are compatible across both brands (e.g. Sram der system with shimano freewheel) Can you give us what model shifters and derailleur is giving you the issue? Also here's the thread where I had the issue if it helps:
http://www.bikeforums.net/bicycle-me...l#post16601000

But your symptoms sound like mine and mine was a compatibility issue. Can't tell you for sure without knowing the models though.

And as stated above, just because both components are Sram doesn't mean they work. You may be using Sram shifters that are meant for Shimano derailleurs.
So you'll most likely need Sram compatible shifters to match your der's. OR replace the der's with something Shimano (since it sounds like the Shimano comp. shifters).