Hello Ardni,
I am not sure I can be much help with this anymore. I haven't worked with the Cyclone (or Quartus) for nearly a year now. I remember though, getting that exact warning you are getting.
The only solution I remember (and I don't even have Quartus installed to check) was something in the settings of the whole system. You need to somehow specify these channels in the settings to use dedicated routing to ensure proper timing.
Hopefully that points you in the direction of a solution. Sorry again, that I am not much help.
Good luck!
Dave