Hello Caecar,
According to my knowledge, you must be getting this error im timing analysis phase. Are you using any derived clocks in your design? Or are you using any PLL's in Cyclone?
This problem is a typical design problem if you are using a derived clock.
I have faced this kind of scenarios with my own designs which; in simulation work fine. Even in sythesis they look pretty, but when it comes to Timing Analysis in Quartus it spits out this error.
Please tell me if you are using two different clocks. If not please explain briefly about the design; I can help you in better way in that case.
For your reference I am giving you some guidelines:
1) This link is from altera support / solutions database. Please give it a look:
https://www.altera.com/support/kdb/rd07061999_3436.html
2) Please search for Application Note 123 "Using Timing Analysis in
the Quartus II Software". Refer to Page 17 in that document. It is >> Advance Timing Analysis > clock skew.
Please tell me if you can't download the application note. I will send you.
I hope it sloves your problem.