Could be an overcompensated probe, too, was the probe compensation adjusted recently?
Cut the trace near the clock pin (at the signal source side) and insert a series resistor of 20...200 ohms. That should reduce or eliminate the ringing. Then observe on a known bad board if the error still happens when the ringing is not there any more.
Also, make sure you have good decoupling 100nF or so, close to the supply pins (near each chip if possible, or as often as possible). For debugging purposes, try to solder a 10-100nF decoupling cap straight to the power pins of each IC.