Ray Tracer delivered "new Bob" from the Web, but no explanation is given as to how he found him in the first place. Ray has no speaking lines yet in season 4 and appears to be otherwise unnecessary to the plot, to the dismay of his fans no doubt.

Mention is made of Phong's scans not being able to tell which Bob is the original. Gee, why not? perhaps Bob's original code is not available for comparison in Mainframe. Also, when did Phong get the chance to run a scan on the new Bob?

In my opinion, neither Bob looks like the original. The last time we saw Bob in "Number 7" he looked and sounded correct. Since then Bob's face has been remodeled with a greater range and subtletey of expression, and you can notice he doesn't look exactly like the Bob from the first two seasons. For example, Bob's eyes are shadowed by his brows more than they were before, making him often appear brooding or troubled.

Matrix continues to go about in game sprite mode any time he's not required to reboot. Perhaps this is to keep his identity different from Enzo's in format so their PID files are not confused with each other's.

The new Bob exhibits no skill or intuition at playing the Patzu Heavy X game. In the last round Bob suggests that Matrix cheat to defeat the User, then Bob himself cheats to end the game. This is a very subtle clue that the new Bob lacks experience he should posess.