I think part of this aspect is actually utilized. During the sidequest for empowering the Masamune, masa and mune reveal the secret of utilizing the power of the Masamune, so from that point onward, its not as though the sword is actually stronger, its more likely that Frog is harnessing it in the way he had done at the Magic Cave.
I'll backtrack a bit to further demonstrate the point. When Frog is at the cave with the purposed of defeating Magus, he has the focus and drive to push the sword to its fullest to complete his goal. However, come time for the gravity well from Lavos' interference, and Frog loses some of that drive, and you find out through events up until the Masamune sidequest, he bears a grudge against Magus, yes, but he has guilts and doubts that keep him from having the focus to use the sword fully up until he meets with Cyrus that one last time. Isn't it phased at the empowering of the sword that its 'full of vigor?" Vigor being effort, energy, enthusiasm. So with Glen's depression past Magus' castle, he can't tap into the vigor of power.