You removed the2.5 install (including config) and did a clean install of 3.0 and re-setup all drivers and re-added all connections/equipment/macros/timers from scratch and it's still giving you the same issue?
If that indeed is the case, which would be very strange, I would try do a clean install and add things one by one to isolate what's giving you an issue. But I have a sneaky suspicion that some remnants of 2.5 is coming back to haunt your 3.0 install.
One of the things I love best about the pi is the SD card -- they're like old Nintendo cartridges, you can swap them back and forth endlessly.
When upgrading to a new version, or even making big changes, you can just use a new card to install/set up the new stuff, and if it fails, just boot off the old one.
