In the modern day of vastly intelligent computer software and important internet presence, it is highly unlikely that a missing middle initial will be the cause of "nonrecognition" of your name. As Stephan wrote, a bigger problem is name confusion; it is definitely a good idea for you to start including your middle initial(s) in future publications. I'll answer here focused more on how to make sure the names are "linked".
My Google Scholar profile, which is compiled entirely by a computer (my only contribution there was identification of duplicate entries and removing them), even picked up some of my undergraduate term-reports which I put on my website many years ago (and which are now no longer available). Of my published papers, I've listed at various times my name as
- Willie Wong
- W W Wong
- Willie W Wong
- Willie W-Y Wong
and I don't seem to have had much trouble*.
If you want better control over the articles associated to your name, you can always register for Web of Science researcher ID and/or an ORCID which are both designed to help alleviate the problem of name collision and name changes throughout the career of a research scientist.
For fields which encourages the use of arXiv, the author identifier also helps group all of your pre-prints, and allows you neat things like a Javascript widget for your own website showing your recent pre-prints.
For mathematics, the AMS maintains author profiles (they recently upgraded this!) to which you can also submit corrections to include omitted paper or to exclude misattributed papers by other authors. (The AMS author profiles are only accessible through a MathSciNet subscription.)
I am not that familiar with other fields, but you should look around to see if your scholarly society provides a similar service to help maintain a comprehensive publication record for authors.
*With Google, at least. Microsoft Academic Search has some trouble coming up with my complete list of publications.
