It was because I had amended the names of the files where they were stored on my computer. Rekordbox reads from where the files were originally transferred i.e. the name they of the file they were first moved from your computer into Rekordbox. I changed the name of the file on my computer from "Electronica" to "Electronica & Nu-Disco". It thus only transferred the files that had been moved to Rekordbox AFTER the name change. Rekordbox couldn't find the tracks from BEFORE the name change. I then re-imported the missing tracks.
I have now kept the files the same names and every time I sync now there is no issue. Hope that helps.