"Could it be that perhaps the correlation between vaccination and NPAFP was because the surveillance was part of the vaccination programme and the temporal relationship was not inherently vaccination -> NFAFP."
You can speculate all you want, since the paper you cited was not designed to test your conjecture. It was an unrelated qualitative study, designed to "We conducted a qualitative research to explore care and support for children with AFP after their diagnosis." They merely interviewed "parents of children with polio (17), with non-polio AFP (9), healthcare providers (40), and key informants from community including international and government officers, religious leaders, community leaders, journalists, and academics (21)".
Some facts that contradict your speculation: It is the systematic AFP surveillance for 10 years before the polio vaccinations campaign in that very state Uttar Pradesh that established the 25-fold increase in AFP following these vaccinations, and 35-fold increase in another polio test state, Bihar. (cf. [1] pp.115-116).
Another interesting quote from the same paper [1] p. 116:
We have seen how polio, that was not a priority for public health in India, was made the target for attempted eradication with a token donation of $ 0.02 billion. The Government of India nally had to fund this hugely expensive programme, which cost the country 100 times more than the value of the initial grant.
So, the way it works is that Gates buys pharma stocks, then bribes few officials in India for $0.02 billion to make their country spend 100 times more on the program. Of course, the pharma makes big bucks not only on the vaccines, but far more on life-long "management" of the diseases they caused, all the while Bill's pharma stocks go up. Having been scammed of intellectual property by Microsoft in mid-1990s, I can see that Bill Gates hasn't changed his "ethics" one bit after moving into the "charity" business. It's same old Bill Gates.
-- Reference
[1] "Indian J Med Ethics. 2012 Apr-Jun;9(2):114-7"].
(full text pdf found via Google)