My Harmony integration has been working for a few months both ways now. I had the same issues early on though. And I have not tried to install any new actions recently. Afraid to touch anything.
My hub and remote just updated themselves to the new firmware today and everything is still working. Out of curiosity I found the release notes which do mention SmartThings fixes (for the desktop/myharmony.com setup software which maybe is what I used previously when things started working, possibly).
February 17th, 2015
Harmony Ultimate Home, Home Control, and Home Hub firmware (v4.3.41)
Support for Nest Protect Sensors, Rheem Water Heaters
Fixed the issue of IR commands intermittently getting buffered
Fixed the issue in Remote showing incorrect time (Users can modify the timezone directly from the Remote)
Fixed the issue with Harmony Hub & Roku in IP mode
Fixed the issue with startup of scheduled Activities
Enhanced the Bluetooth connectivity between Harmony Hub & Sony PlayStation 3, Amazon Fire TV, Fire TV Stick
General Bug Fixes
MyHarmony Desktop Software and MyHarmony.com
Fixed the issue of login freezes at 75%
Support for adding SmartThings, Lutron & Honeywell on applicable Harmony Remotes
Remote customization of Ultimate, Ultimate Home, Ultimate One, and Touch will be retained after a USB Sync. This includes:
Screen lock
Settings Edit lock
Remote keypad brightness
Remote vibration on/off
Remote vibration effect
Remote tilt sensor
Fixed an issue with button mappings getting lost in Harmony 350 after teaching IR commands
General Bug Fixes