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Immibis' Microblocks integration causes bugs in Immibis' Microblocks #666
What seems to be happening, from my initial glance at the code, is that AE2 overrides the part placement code with its own for non-AE2 tiles (that is, any tile entity), which causes synchronization bugs as it's not how you're supposed to be doing things.
...also, I got the worst possible issue number.
I suspect the AE2 container block then deletes itself since it doesn't contain any AE2 parts, but I haven't delved into that code yet.
Again, everything in this comment has not been verified.