Could you provide screenshots of the blueprint you are using to spawn these ISMs? I attempted to reproduce this in a clean project and was unable to do so.
I then did a print-string for the Array (on both versions) and i came to the conclusion that the “set array element” with “0,0,0” did set random values until it got a variable with 0,0,0 attached to it.
So the ISMs are spawned according to the rotation in the array, but the rotation gets set wrong after Nativizing. (not 0,0,0 as it should be.)
But i cant replicate it (at least not today) since i replaced the 0,0,0 with a variable that is 0,0,0, even if i remove the variable. (tried it 3 times now)
This is an issue where nativizing blueprints caused uninitialized values to be replaced with a temporary value. The workaround you suggested (using a variable instead of just the default value on the pin) will work fine for the time being.