I don't think background checks system broke down. It's fairly robust and it is near instantaneous these days, we are not in early 2000s anymore.
Looks like delays are linked to ELIS failures (ELIS before DACA applications only really dealt with low volume applications such as green card replacements), but I am not sure if background checks are completely independent or if they rely on info to/from our application and if this connectivity broke down for the early applicants.
Guess we'll never really know as USCIS only mentioned "technical difficulties".. admitting that on their website is already a rare step.