It looks like nta-recheck (7s) in the system test is too small for this system.
Note the time stamp in ns4/named.secroots  is already past 14:48:26.000
which is when badds.example/_default expires.

I:checking positive and negative validation with negative trust anchors (123)
I:ns4 Negative trust anchor added: bogus.example/_default, expires 24-Oct-2017 04:48:36.000
I:ns4 Negative trust anchor added: badds.example/_default, expires 24-Oct-2017 04:48:26.000
I:ns4 Negative trust anchor added: secure.example/_default, expires 24-Oct-2017 04:48:32.000
I:ns4 Negative trust anchor added: fakenode.secure.example/_default, expires 24-Oct-2017 04:48:32.000
server reload successful
I: dumping secroots
I:failed - with NTA's in place failed
I: waiting for NTA rechecks/expirations
I:failed - checking that default nta's were lifted due to recheck
I:failed - checking that default nta's were lifted due to lifetime

more ns4/named.secroots
secure roots as of 24-Oct-2017 04:48:26.412:

 Start view _default
   Secure roots:

./RSAMD5/48623 ; trusted

   Negative trust anchors:

bogus.example: expiry 24-Oct-2017 04:48:36.000
secure.example: expiry 24-Oct-2017 04:48:32.000
fakenode.secure.example: expiry 24-Oct-2017 04:48:32.000