I'm assuming these are:
- separate controllers,
- each connected to their own separate arrays,
- with both charging a single battery bank.

If so, a couple of possibilities occur to me:
1.  Each controller may be reading bank voltage slightly differently (a few 10ths of a volt - more than that may mean a wire issue).  Measuring & comparing voltage while charging at both the battery and each controller output terminals may help in troubleshooting.

The lower reading controller will output enough current to hold bank voltage in absorb or float at what it sees as the right voltage, but at what the high one thinks is "too high", so the high one outputs nothing while it waits for bank voltage to drop to the "right" voltage.  Not sure about your controllers, but my MN Classics have a setting to adjust for these minor variations so they all see about  the same bank voltage. 

Small differeces don't really matter all that much though, as most of absorb and float uses diminished current, and one controller can often hold voltage alone.  

2.  If this is happening in bulk before either controller reaches absorb though, I'd look for possible issues with the non-producing array (eg shading, wiring issues, etc) or the controller (eg open output breaker, etc).

Alan,
If you are at the site might I suggest:   Turn off both p.v. array input to the charge controllers, turn off mode(input), then turn off power to both charge controllers , wait a few minutes , turn on power to controller having the problem only,  wait a minute or so,turn on input mode,  turn on array breaker for this controller only.  Now see what happens, reasoning....rebooting sometimes will clear the problem, and with the working charge controller idled the suspect controller should go to bulk and start charging, it won't be affected by the working controller.  Let forum know what happened with this test.

Please note....I'm a MidNite guy, with limited exposure to Outback gear,  but based on the same team designed both, they are similar ....I'm not familiar with Outback Menu system.  I'm not sure how Outback turns off input. It is important that the controller is powered up first before applying solar input.  

When I have both Classic 150's charging one bank they will split the load on bulk, but even with follow me they do not exactly split the load, very minor differences in settings will leave one doing most output. At float the lead classic does the bulk of the work. Even changing the "factory calibration settings" it is very difficult to get them to "exactly follow each other".   Bottom line is I am floating before noon.  I have two main banks of L-16 and leave them separated most times,  and charge each with their own sources of power.. Esseciantly I have 100% redundancy..two complete systems but one main inverter witch can be powered by either system alone for most uses.......but when I have a big project which will max out my big inverter then both banks are paralled, household loads are switched to the Cotek SK-1500 inverter and the MagnaSine powers the workshop. Too complicated but I built it peice by peice.  I just can't pass up a set of Rolls Surettes S530 L-16's for $20.00 even if apparently dead....They will be 14 y.o. In a few days!  Still testing as new.....I'm very hands on with my system...tinkering it constantly .....I've not had a day without power for years now..reasoning behind not just leaving them in parallel,  they are not a matched set, close but no match. The Surettes end up being overcharged and the Interstates haven't yet finished absorb after a few weeks left paralled.  Both sets are L-16's but manufacturing differences between Rolls Surette  and Interstate (Johnson Controls) make it impossible to get an exact match. Much better results in not paralleling them unless nessecary for that big power day. My system is 4   times the size I need for household use alone. 

Alan,
Sometimes a complete system shutdown and restart will clear out accumulated errors. Complicated electronics are like computers in a way, they will build up unneeded data which they will stumble on, system shutdown and restart is kinda like a new day....