They are both a year apart but have still remarkable similarities, especially in the layout but also in the results.
The first study, from March 2003 was the one to which I was referring in the previous 'infections' posting, yet the one you were referring to was only accepted in December 2003 and published in May 2004. Again, many apologies: it comes from reading too many papers in too short a succession. If you care to look back at the 'infections' posting, you will see that

Anyway, in short, the 1993 study, involving the Nurses Health Study found, in summary, "....a positive association between serum titers of anti-Cpn IgG antibodies and the risk of MS. This association was stronger for progressiveMS than relapsing remitting MS. It remains to be determined whether Cpn infection or reactivation precedes MS and influences the progression of the disease."
The 2004 study, involving US army personnel and KPMCP, found, as you say, "Neither Cpn seropositivity nor serum anti-Cpn IgG antibody titers predicted risk of developing MS. However, due to the heterogeneity of results between cohorts, we cannot exclude the possibility that infection with Cpn may modify the risk of MS."
The Munger, Ascherio group now seem to be moving on to researching into vitamin d and its role in MS. It will be interesting to see if they come up with anything new here.
You say that you are an eternal sceptic, but a hopeful one. It is good to be a hopeful sceptic, in my opinion. I came upon the antibiotic treatment with hardly time to think about it: David brought the doxycycline home one evening about a week after diagnosis and said, "right, try this!" So I did, not really thinking that anything would come of it: definitely a sceptic but not hopeful. Unusual, because I am a natural optimist.
Incidentally, If you can get hold of the Rogier Hintzen paper it is very well presented and worth reading. We have a hard copy here but I can't lay my hands on it.
Sarah