Transfer UV layout, render to texture issues

[arhurt]

Hi, I'm using the technique shown here to fix a model I've made. The current model uses 2 large texture sheets that I must change into 3 smaller sheets so that I can save up on Alpha channels.

Now I'm having problems at some point, and I think it is related to render to texture.

Here is a part of the model that I must transfer to a new UV:

And here is the result I get with the baked diffuse map on the new UV:

Here is a comparisson of the original texture sheet side by side with the new sheet created from RTT (original on right):

I'm not sure what could be wrong, if you have any idea, or if this is a common issue, let me know. Thanks a lot.