I have re-transformed the plasmids into EPI400 cells and verified by digest that the LacO repeats are intact in the original version of the plasmids. The plasmid was resubmitted to Addgene 9-26-2013 and the fully intact plasmid should be available for distribution shortly.
The vectors pCFJ1324 and pCFJ1319 in the miniMos kit contains a 256x LacO repeat. When we digested the vector it was the correct size but the repeats are prone to deletion when propagated in bacteria. Mike Nonet has digested several colonies from the kit distributed by Addgene and it appears that the bacterial clones being distributed have almost no LacO repeats.
I will re-transform the vectors into EPI400 bacteria, that keep plasmids at low copy number until induced with arabinose. If that fixes the problem, I will deposit the bacterial strain again.
Sorry for the inconvenience.