If the CPU speed is set to 1 MHz, Run/Stop-Restore resets it to 3.5 MHz, very likely because it is resetting VIC registers that include FAST but not VFAST. Run/Stop-Restore should also set VFAST to return the computer to the boot state of 40 MHz.
It's debatable whether Run/Stop-Restore should affect the CPU speed at all. I think it should, as a matter of restoring portions of the boot state.
If the CPU speed is set to 1 MHz, Run/Stop-Restore resets it to 3.5 MHz, very likely because it is resetting VIC registers that include FAST but not VFAST. Run/Stop-Restore should also set VFAST to return the computer to the boot state of 40 MHz.
It's debatable whether Run/Stop-Restore should affect the CPU speed at all. I think it should, as a matter of restoring portions of the boot state.