G’day! First, beryllium is a metal, not opal. Possibly they are the
opal (and/or fluorite) from the Brush-Wellman beryllium mine in Utah?
Anyhow, if they are slabs, them possibly the odor could be from the
oil in the slab saw; some of the oils are quite smelly and if not
washed off well, they persist. Or it could also be the pesticides you
mention, although if the smell doesn’t wash right off I would doubt
it, unless they were actually soaked in the pesticide.
In either case, since whatever caused the smell is probably oily, or
at least organic, you should be able to wash it off using some of the
orange soap (get it at an auto supply store) that rockhounds usually
use to wash off their slabs after cutting them.
BTW, if the “berylium opal” is what I mentioned above, it may have
small amounts of metallic beryllium in it, and since beryllium
(especially in fine particles, that you could breathe in when cutting
it) is rather poisonous, you need to wear a good mask when you cut