Some discrepancy (up to 25% or so) is normal. It's also normal for this discrepancy to be more exaggerated during the site-wide freeleech period, which is happening right now, due to heavier traffic during this period. If you see any seed discrepancy, you should expect your leech statistics to show similar differences, percentage-wise.
The exact cause for any discrepancy can rarely be determined because there are many factors that play a part in the cause.