Yes, the ALTMEMPHY megafunction does not correctly support periodic ZQCS (zq calibration short) commands for multiple ranks where any of the ranks are arranged such that they share the ZQ resistor. To fix this issue one is required to do the following steps:
1. Open the <variation_name>[_phy]_alt_mem_phy_seq.vhd file
2. Search for the "ZQCS" function and find it's use within state s_zq_cal_short (this is within entity <variation name>_alt_mem_phy_admin)
3. Change the "2**MEM_IF_NUM_RANKS - 1" ("2**MEM_IF_CS_WIDTH - 1" for levelled PHY) operand to the function to the operand "2**current_cs"
4. Save the file and if you require to simulate this change in a "verilog only" simulation setup then re-simgen the PHY as described in the External Memory PHY Interface Megafunction (ALTMEMPHY) userguide (PDF).
The above solution applies to both the levelling and non-levelling enabled PHYs. This issue will be fixed in a future version of Quartus® II software.