The RUNSQL command was officially released with V7R1 but was made available to V6R1 systems via PTF.
After our system was upgraded to V7R1, I was no longer able to compile any CL programs using RUNSQL for V6R1 compatability.
According to IBM (who handled the upgrade for us), they don't automatically install V6R1 compatability because they don't know if the V6R1 PTF was applied beforehand.
The official solution is to create a duplicate object of the RUNSQL command into the QSYSV6R1M0 library following the V7R1 upgrade.
My question to IBM on why they simply do not do that as a standard part of the upgrade process have yet to be answered.