I've heard of other people having this problem so it's not unique. I agree with all that Hate said in that you may just be putting to much thought into blinking. Is there any particular reason that you can think of for why you do it now when you become lucid? I don't want to presume anything, but could there be an automatic fear response remaining from when you were younger and had bad dreams.

If that's the case, when you reach lucidity, focus yourself on the dream and repeatedly tell yourself that you are dreaming. Get involved in the dream right away and take control. Don't give yourself time to let emotions get in the way.

*waits for mind to wake up* Well, that's about all I can come up with right now.

-Amé