It seems like the QueryResult is always to 1.
Reproduce (It is the copy of the commands I used)
/summon ArmorStand ~ ~ ~ {CustomName:"__weathermod"}
/scoreboard objectives add temp dummy
/scoreboard objectives setdisplay sidebar temp
Clocking Blocks:
/scoreboard players add @e[name=__weathermod] temp 0
/stats entity @e[name=__weathermod] set QueryResult @e[name=__weathermod] temp
And when u then type
/execute @e ~ ~ ~ time query daytime
it is only 1 in 15w37a, even through gametime is not 1.
It worked perfectly in 1.8.8
Cannot reproduce on 15w39b. Does the issue still happen for you?