Due to a problem in the Quartus® II software version 11.1 and later, the EPE may show an incorrect number of HMCs when the EPE imports the .csv file.
The Quartus II software can generate the .csv file which has design information using Generate PowerPlay Early Power Estimator File under Project menu and the EPE can import the .csv file.
When there more than one HMC with the same configuration in your design and the EPE imports the .csv file, you may see only one HMC for each HMC configuration in the HMC tab of the EPE.
For example, when your design has 2 instantiations of an HMC with x16 DRAM width, 1 command port and x32 Fabric Interface width at 533MHz, you will see only one HMC with that configuration in the HMC tab of the EPE after importing the .csv file.
When the number of HMCs is incorrect in the HMC tab of the EPE after importing the .csv file to EPE, manually add the HMC configuration according to your actual design.
This problem is scheduled to be fixed in a future version of the EPE and the Quartus II software.