Hi-ya Christian,
My 660Ti registers at ~270 khash/s peak (scrypt) for a single instance of cudaminer (which appears to start a single mining thread) - By starting two instances, I'd have expected that rate to halve. Instead, each instance reports ~200khash/s peak.
This is surprising. What is your launch configuration?
What does GPU-z show for GPU utilization when running just a single instance?
How's GPU utilization and memory usage with 1 and 2 instances?