Bit of an issue with the new firmware. It turned off the effect loop on all patches by default. Took me a while and a lot of head scratching to work that out. Had to go in and change all the settings to 'post reverb' to get my looper registering again. No idea why that worked - on my Mustang the choice is pre or post pre-amp, and that works in a way I actually understand 
Howard, is this the Firmware [ Ver.2.01 ] Dated OCT 2017 ? Released around the time this thread was started.
Or the Newest one [ Ver.2.02 ] Dated NOV 2017? This one has a few bug fixes, namely,
Update history
[ Ver.2.02 ] NOV 2017
Bug Fixes
The following bugs were fixed.
•When TONE SETTING is set to "PANEL," after using the GA-FC (foot controller) to set respective effects to "OFF" and then again selecting "PANEL," the respective effects return to "ON."
•Selecting a TONE SETTING for which EQ is set to "OFF" yields sound for which EQ is set to "ON."
•When a MIDI Program Change message and Control Change message are received simultaneously, the Control Change message is not applied.
•When the unit is updated to version 2.01, all TONE SETTING Program Change numbers are set to "1." (This occurs when updating from version 1 to version 2.01.)
* Use BOSS TONE STUDIO for KATANA Version 2 to set the Program Change number for each TONE SETTING.
•When the unit is updated to version 2.01, the SEND/RETURN values for BANK A and "PANEL" are set to "OFF." (This occurs when updating from version 1 to version 2.01.)
* Use BOSS TONE STUDIO for KATANA Version 2 to set SEND/RETURN to "ON."
https://www.boss.info/us/support/by_product/katana-100_212/updates_drivers/4b233e0e-e986-494f-9e1f-11ee766679b4/