I had a similar experience. 499 and then 497 on FL 1 and 2– needless to say I was pretty discouraged. I decided to take a few weeks to just do solid content review, and did some mixed practice with EK 30 min exams; I started seeing a lot of variations between the Kaplan and EK testing styles (EK is way more experimental-based). So where I was hitting 124's consistently on Kaplan, I was hitting anywhere between 127-130 on EK. Granted those are only the 30 min tests that I've done for almost every lecture in almost every book, but the confidence definitely helps.
But as much as the test is knowing content, I also really think it's being familiar with the test itself. I recently did FL 4 from Kaplan and received a 505 (128 in bio) and still think it's just test familiarity and practice with timing. I'm going to do another Kaplan FL this Saturday and then start to do ~2 a week plus section banks/question packs as well.
TL;DR don't get discouraged by practice test scores.