That's most likely the problem. For the moment, the easiest way is probably just to do a search/replace on the KRL file.
E.g. search for "E1" and replace all with "E2", then search for "E2 0.0, E3 0.0" and replace with "E1 0.0, E3 0.0". I may be mistaken, but if I remember correctly the KUKA doesn't worry about the order of variables, i.e. if its XYZ or XZY.
On the long term, you can reconfigure the external axis from E1 to E2, or wait for a future KUKA|prc release for which we are planning to support more than one external axis.
Johannes @ Robots in Architecture