this one helps. I found a way to fix my problem (not entirely, but sufficiently for my need). This issue only occurs when I use custom lables pulled from somewhere else; if I use generic "1,2,3,4,etc." the graph stacks properly and shows data. Ideally I would have custom lables, but I can just put a simple table beside the graph to act as the axis labels.
jqPlot - How to add vertical scrollbar to legend box containing many legend items
To fix this issue I found some people on the web mentioned some issues with overflow on tables in IE, but I couldn't get a needed answer. Therefore, my approach was to wrap the table into another element. I wrap it in a div and set appropriate values on it and it works cross browser :)