The series R or L in the S299 clock line (that you mentioned are present in respective later models) are there to suppress parisitic oscillation / ringing.
It may be that ringing - even if not going negative - is upsetting the internal transitions somewhat, for example resulting in some overlapping conduction in totem-pole drivers, and may well be why they added the series R/L in later models. If you wanted to experiment, you could try raising the IC a fraction of an inch on some extenders** - except for the clock pin where you shall insert a small-Ω R in series as the later model did (was it 36Ω?), you don’t necessarily have to find an L. Or if you’re careful you may even avoid extending the whole IC, by bending the clock pin on the IC out just far enough so it misses the socket pin while inserting the IC, and connecting the R in series (close in, not on long clip leads, could tack-solder one lead to the IC pin, then a fine wire on the other lead with a piece of slide-on insulation to get down between the legs to the socket pin). ** individual pins from machine-pin IC sockets can be nice for this, or an IC socket with wire stubs, or wire stubs soldered to IC pins seeing as how the removed IC is already solder-tainted, just use wire small enough not to damage the socket you're inserting into.
