Wow that's terrible!
I guess that future applicants should take a lesson from this. Since some schools allow you to call and ask about received materials, make sure you check whether both the general and subject scores are on your score report. I've seen several posts from the past few years of students saying they found out late in the process that all of their schools received an incomplete score report. That's a scary situation to be in.
While some schools using embark have the online notification system, since sorting materials is often done by a central admissions office that won't know whether we need subject scores or not, they're probably just confirming that "yes we have a score report," not that it contains all the necessary information. So again, make sure you confirm with at least one school that the report is complete! Chances are, if one is complete, the rest are.
That's pretty irresponsible that Stanford didn't contact zxcv in December like they said they would if something was missing, and especially rude considering they have the highest application fee I know of and demand two official transcripts when they could just make a *** copy!