Dim.. Pause.. Bright.. Pause.. Dim Pause Bright. And so on indicates one of two things
1: A circuit breaker cycling (Self resetting thermal type)
2: A converter switching between bulk and absorption..
WFCO's do have a high failure rate (recommended replacement is Progressive Dynamics 4600 series, only replaces the electronics, you still use the WFCO power distribution panel. NOTE Progressive Dynamics is a US Company. they manufacture in Michigan. I have visited the factory. )
However if you just replaced the Converter. I would also suspect the batteries.
Can you measure battery current? I have a Crafstman Clamp on AC/DC ammeter. yes the clamp on reads DC as well as AC... (One interesting fact is I've seen "Clamp on" DC ammeters that not only indicated current flow, but direction, (I do not think this one does direction) from back in the 1950's.. Ford used them).