I'm using Coldfusion 9 and it works fine for me.
isNumeric(1e-06); // true
jsn = '{"string":"foo","number":123.456,"scientific":1e-06}';
struct = deserializeJSON(jsn);
writedump(struct);
You can try to run isNumeric(1e-06) to double check if it's picking it up as a number in scientific notation.
As I said, it works fine for me in Coldfusion, but it might be a bug in Railo: https://groups.google.com/forum/?fromgroups=#!topic/railo/tzwII5e0caQ