What are you talking about, no it wasn't from X-Factor up until NXM, Marvel was adamant that she stay disconnected from the PF and moreover that she never had a connection to the PF. There were literally several series and stories such as Excaliber, Inferno, the Onslaught Saga, and the arcs during Revolution which specifically stated Jean was NOT the Phoenix nor was she tapping into its power.
However Jean still independently manifested the Phoenix raptor at least twice during X-factor and several more times in the 90's all WITHOUT having access to the Phoenix. During Revolution, her telepathic powers became so great that they naturally manifested as a Phoenix Raptor which could affect physical matter but she wasn't connected to the PF. She didn't tap into the PF again until NXM, and that was AFTER her secondary mutation which returned her telekinesis.
During X-Factor:
Against a young lady manifesting a raptor, Jean created her own.
During the 90's:
During Revolution:
All of the above was done expressly without accessing the PF.
Seagle was the only writer before Morrison who wanted to reintroduce the PF, but in-story he never got the chance to do it. She was Phoenix only in name and costume of which she initially did for Rachel.