From a quick check, it looks like the issue is probably a change in when the “handled” property gets set. (Unfortunately, my copy of 6G60 is hanging up when I try to open the Standard Rules, so I can’t make sure.)
In 6M62, a thing will be set to “handled” as part of the standard taking rule, during the Carry out taking phase. That means that when you check whether it’s handled in the After phase, it’s already been set to handled, even if this was the first time you took it.
It looks like you can fix this by changing “is not handled” to “was not handled”–the “was” checks for whether the condition was true at the start of the turn. See §9.13 of Writing with Inform.
Use scoring.
Lab is a room. A flashlight is in Lab.
After taking the flashlight when the flashlight was not handled:
say "Good idea, you might need it.";
increase the score by 1.
Also this is a bug in the documentation, as §9.2 recommends awarding points in exactly the way you do it. I’ll report it!