Lubricant would certainly have been used on the cutting wheel. There is really no telling what it could have been exposed to in their shop.
When I build my vivs from scrap glass, I cut the panes and sand the edges, then wash them with just a little liquid dish soap. Rinse them VERY well, dry them, and finally, they get a wipe-down with rubbing alcohol and a soft clean rag.
I have no idea what may have been on a pane before I got it, so I treat every pane as if it is contaminated.
Glass itself cannot be the problem. It has to be something on the glass. We've already covered a possible contaminant. A bacterial film growing on the glass could also be nearly invisible, yet cause a smell. If it's been on the viv for days, that could be a potential issue, but if you noticed it right away, you could rule that out.
It could also potentially be that now that the viv is better sealed, it is collecting and concentrating the natural smells in the viv, which then rush out with the warmer air trapped under the lid, upon opening it.
A description of the odor might help...chemical? earthy? foul and rotted? Oh, and how long was it in place before you noticed it?