This is related to MC-2340 and MC-2202 but are too old and don't describe the problem concisely anymore, and they seem to get no attention because of this.

"One tick physics" seem to be broken or at least behave very unintuitive.
This issue was introduce around the "Redstone Update" and hasn't changed since.

Some examples:

http://www.youtube.com/watch?v=Z0OsUjZXQVs :
A clock is connected to 12 circuits which are logically the same (except for placement) but have different output

http://www.youtube.com/watch?v=CgPIavyc4ig :
A (comparator) clock is connected to a repeater chain, only after 3 redstone dust beginning from the comparator the repeater receives the correct signal, before the repeaters are always in active mode.

http://www.youtube.com/watch?v=Ac_IujHfXpw :
A clock is connected to 4 repeater chains in all directions.
Two of them get the correct signal the other two are wrong.

And for me the most important
http://www.youtube.com/watch?v=JNTTuGOqJkg :
A locked repeater chain (used as a shift register) corrupts the signal stored after the lock is released.