Well somethings probably still different between the programs. It might be worth comparing the gcode files from each program to take a closer look. You can check things like the F-values to see what speed the first layer prints at. You can check the Z-values to verify what height the printer is going to. If you print a really simple cube or something like that, it should also be pretty easy to check the extrusion amounts/widths to make sure those match. And obviously cooling and bed/extruder temperatures are easy to see too.
That's what I would do if you really want to figure out what's different. If the gcode is the same, then the printer should behave the same way.
Also - I've definitely made the mistake before of claiming something worked previously, but then when I made this one change it stopped working. However, sometimes there are other factors involved. For example, maybe the bed is just dirty or something like that. So make sure you occasionally re-print a file from your other software to make sure it STILL works. That just helps rule out other factors and may save you some headaches