I guess I'm confused as to why you would use a generic part instead of the 74LS00/08 parts. What you are seeing is the differences in the timing parameters. If you double-click the generic AND gate and press Edit Model, you will see the rise and fall delay is 1nS. If you place a 74LS08D and do the same thing, the rise delay is 15nS and the fall delay is 20nS. More then likely, there is a spice parameter for the counter where the QD line goes high for a very small amount of time while the QA, QB, and QC lines transition from high to low. The real AND/NAND gates can't see this transition due to the propagation delays (rise and fall) inherent in the actual part. If you change the generic parts values to that of the actual component values, the circuit should work.
