The glyphosate link is interesting. Of course that herbicide has been the object of a huge load of hype (biodegradable, innocuous, etc), but interesting things are surfacing here and there about it. I doubt you'll have missed last month's publication by Barney Gordon of Kansas State (no less!) showing manganese uptake deficiency in RoundUp Ready soy (explaining lower yields than conventional soy).

Gordon (from the Google cache, the pdf is for some reason disabled...)

There is evidence to suggest that glyphosate may interfere with Mn metabolism and also adversely affect populations of soil micro-organisms responsible for reduction of Mn to a plant-available form. Manganese availablity is also strongly influenced by soil pH. As soil pH increases, plant-available Mn decreases. It is unlikely that Mn deficiencies will occur on acid soils. It stands to reason that the addition of supplemental Mn at the proper time may correct deficiencies and result in greater GR soybean yields.

Quite un-glyphosate-connected, my neighbour who grew 50 hectares of GM BT maize last year - MON 810 - had fusarium problems with it. This makes it officially unsaleable in France because of the microtoxins present. (Spanish buyers are less fussy and the crop just went South of the border). Where there might be a link is the effect on soil micro-organisms of the transgene from bacillus thurengiensis, which is a... soil bacterium.