Who said he lied? Fitzgerald, who knew from the beginning exactly WHO "outed" Valerie Plame?
Scooter was deposed, and allegedly lied about what he said to three reporters, per their testimony. That is the prosecutor's case - nothing more, nothing less.
Remember there are five counts.
Count 1: Obstruction of Justice
Counts 2-3: False Statements
Counts 4-5: Perjury
This mostly appears to be based on Fitzgerald's interpretation and timeline and his apparent belief that Wilson was right about it all being a personal vendetta against him (Wilson).