GT ores are tile entities (for the reason that there are too many combinations of them to not occupy most block IDs)

My policy generally with tile entities is just never to overwrite them. It was convenient earlier on to avoid certain problems. It's working as intended in that sense.

It may be worth tackling this, but it's mostly just a problem with GT ores. I'll have to think about it.

Consider using .hasTileEntity() and then removing tile entities manually before removing the block.

Just to follow up, this has been implemented and will be in the next release.

I made it delete all tile entities except chests and spawners.