In case this helps in the meantime (while they are still working on the fix)...
When the .csv comes up with UNIX epoch time in the Lateness column, it appears to be
( ScheduledTime + Minutes Late )
or in other words the projected timestamp of the departure.
I believe it's always been
( Lateness >= ScheduledTime )
as long as the epoch timestamp has been showing up. Because of that, I implemented a work-around by simply taking the difference between the two
( Lateness = Lateness - ScheduledTime ) if ( Lateness > 1000000000 )
and that's been working well. (Note that not all of the Lateness values have been showing up with epoch time. Some are still showing the minutes delta like before.)
One note for the MBTA folks: The Departures feed still seems to have the leading-zero for Trip numbers the way the schedules were prior to May 23. For example right now the feed has Trip 023, 047, 087. I also implemented a quick work-around for that.