When you talk about "putting the .jnl file aside" what are you doing?
Stopping named THEN deleting the .jnl file? Using rndc sync -clean <domain
name> ? In the case of the rndc command, you don't need to cycle named.

What user is named running as? Are the directory permissions for the
directory housing the .jnl file correct?

> I am getting the following error on one specific domain and I am unsure
how to fi it. Searching for the error lead to suggestions about not running
> multiple copies of bind on the same machine, but that is not the case
here (and it is only affecting one domain).

> named[652] malformed transaction: example.com.signed.jnl last serial
2018022385 != transaction first serial 2018022384
> named[652] zone example.com/IN:
zone_resigninc:dns_journal_write_transaction -> unexpected error
named[652] malformed transaction: example.com.signed.jnl last serial
2018022385 != transaction first serial 2018022384
> named[652] zone example.com/IN:
zone_resigninc:dns_journal_write_transaction -> unexpected error

> If I put aside the jnl file and stop/start bind the error goes away, but
eventually it comes back, always for the same domain.

> (Setup is DNS primary on on machine and a secondary server on a separate
machine. Errors are on the primary server.)

> --
> Thunder rolled... It rolled a six.
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