Recovering wallet from twelve key words

[Ulysseus]

Okay I recovered my wallet using the twelve key words, on a fresh Ubuntu install. If I use Python wallet-tool.py -g 100 wallet.json. And blockr in the cfg file everything is ok. But the moment I try to use the Bitcoin core ver 0.13 It shows a balance on Bitcoin-qt (which is too low) and python wallet-tool.py wallet.json shows a zero balance. I have tried bitcoin-qt rescan a number of times. Nothing works. Pretty sure this is a simple incompatibility with the Bitcoin core. But it means I can't run the yield generator with Bitcoin core just blockr

[AdamISZ]

It could be just that you haven't rescanned against the new Core instance. Generally you need to rescan only once, at the beginning. I'm not sure, but it seems to fit your symptoms.