We have now tried using the subscription 8.1 of Quartus II. However, we still see the same result. There are 9 clock nets found in TimeQuest, according to above.
However, when using the triple speed MAC I think the altera_reserved JTAG pins are used, I found the below on the web:
"The altera_reserved_tck pin is automatically generated for a design that uses a JTAG accessible module such as the SignalTap® II logic analyzer, the In-System Memory Content Editor or the Nios® II debugger."
I suspect it has something to do with the JTAG accessible module above since the altera_reserved pins show up, but I cannot say for sure. I am in a discussion with Altera on this, so we have to wait and see what comes out from that discussion. I'll keep this updated as soon as I know more.
All advice are most welcome!