Posted this in Proposed Addons w/ the Advanced Miner as this was with the Advanced Miner but the Mod Creator posted that the bug may be in the IC2 code.
I was mining until pipe 10 and then the miner started just outputting cobblestone and filled a chest to capacity and then just started throwing it outdoors.
I took the drill out and put it back in and miner went to pipe 7 and then did the same thing.
Then I just quit the operation and set the miner up in a new location and now it seems to be working normally again.
Don't know if this is a bug or just a conflict with another mod, just thought I would post what happened.