From my experience it's actually very hard to affect film by making it go through airport X ray machines. Unless you are using extremely sensible emulsions you should not notice anything at all (Even in those cases I have heard about people not noticing a thing in 3200 rated film that went through an X ray machine). Plus, if it was an X-ray issue the marks would not be in the exact same place every time, and the fact that it's only noticeable when scanning the film makes it all more suspicious.

There are other things you should consider checking first. For example:
-Is your scanner working correctly? Try to scan a negative without an image or a white piece of paper and see if there are marks on the images.
-Is your camera or lens working properly? Is your lens deformed or has your equipment gone through very harsh conditions lately? This is unlikely, but you never know.
-Where and how do you store the film? Light may have leaked through without you noticing.
-When and how did you first notice the problem? Did you do anything before that (Like changing settings or moving the scanner)?

All these things are actually more likely than the X-Ray theory and it would be a sensible idea to consider them first. I am willing to bet the scanner (And not the film) is the issue here.