Hi,
well there are two packages
- QuartusII as the design software package containing the programmer (Tools => Programmer) and a SignalTapII (tools => SignalTapII Logic Analyzer)
Both are using the JTAG I/F to either configure (Programmer) or configure and upload signals for debugging (SignalTap II)
- the standalone Programmer that only includes the ability to configure while the pof/sof File must be available.
Thus you can use both tools to programm the device, depending on your intention...
Regarding your initial problem - this is well known with "pre 12.1" versions (at least for the WebEdition) and is caused by the wrong driver / JTAG Server (32Bit edition) being installed while not working with the 64Bit edition. Either with installation of most recent 12.1 SP1 WebEdition or the most recent Stand-Alone Programmer this issue gets fixed. You just may not install the 10.1 version once again after having installed the 12.1 SP1...
Even with the 10.1 subscription I would install the 12.1 in parallel as normally this installation fixes the issue and allows you to use the 10.1 subscription afterwards. (IIRC some stuff is reconfigured when starting 10.1 first time after installation of 12.1, while this is nothing to worry about).