I predict that you have either used yyaxis or xxaxis, or else that you have use the older plotyy(), or else that you called axes() more than once with overlapping Position. In such cases, you would have multiple axes in the same location. However, your ylim() call is only affecting one of the axes, so it is getting out of synchronization for labels with the other.
This kind of problem was more likely to happen with plotyy() or calling axes() multiple times.. yyaxis() and xxaxis() are more careful to put the tick labels on opposite side of the graph.
