Cassandra query performs differently at different times
primary key (empID,uniqueID)



  This CF contains data for more that 5K row entires and and each employee contains minimum of 100K columns and the maximum of 1000K columns


That's WAY too many rows per partition.  My guess is that the query slowdowns happen when large partitions are queried.  It all depends on data cell value size and data width, but as a general rule, I would not model more than 10k-30k rows per partition.

To test this out, you could run nodetool tablehistorgrams on your table to gauge things like max cell count and partition size.  Then run your query against both small and large partitions with TRACING ON, and I'm sure you'll see the difference.

Basically, try reworking your model for smaller partitions.