This is off-topic for TeX-SX but IEEE article submission is always weird and unpredictable. Contrary to my comments above, now I've realized that Cybernetics C is using ScholarOne instead of PaperPlaza which is again ... great.
And additionally there is a change notice in the login page
NOTICE: Starting in January 1, 2013 the IEEE Transactions on Systems, Man, and Cybernetics Part C: Applications & Reviews is renamed to IEEE Transactions on Human-Machine Systems. The IEEE Transactions on Systems, Man, and Cybernetics Part C do not consider any new papers, authors are requested to submit manuscripts to the new SMC Transactions. For details see http://www.ieeesmc.org/publications/Scope_of_the_SMC_Transactions.htm.
In any case, since IEEE adopts blind review method (as opposed to double blind) there is no need for anonymizing the article. Thus, journal submissions are done via PDF files and reviewers see the PDF output. In fact you don't even use one column double spacing version since the system checks for the 17 page limit directly (you pay 175 USD per extra page over 12, for the page nobody prints!).
After the review process, the submission is forwarded to the publisher and then your TeX nightmare begins. The current situation with most journals is that you provide the TeX file the images (if any) and other related material as a
.zip file and the publication office compiles it for you. Then you receive an email to proof-read the uncorrected proof and (I'm not joking) you annotate the resulting PDF or submit a separate document about the changes. Then the publication office sends you the result once again as many times as necessary.
Citing IEEE.org header;
The world's largest professional association for advancement of technology.
and this is how they handle the publications.