When I am having problems with threads skipping, I do what Connie suggested--I rethread my machine, and check my bobbin. Always a great place to start troubleshooting.
I just took my first long arm class and the instructor said that some Batiks are more picky about thread than others. Could it be the weight of your thread? Some Batiks are very tightly woven and you do not want to be tearing the fabric with your needle and thread.
I am sorry--these are my only suggestions. Others on the board are long arm quilters and can be more help, I am sure.