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Hello Kate,
Can I ask for clarification on your request? Could you perhaps post a screenshot of how you want the chart to look after you have tweaked it in the advanced chart options (you can post a message with an attached JPG or PNG file)?
FYI, I have just posted a new version of LEAP (2014.1.25) that does improve the display of chart labels and markers. In particular, w.r.t. labels it now plots them with a smaller border making them easier to read and also allows you to plot the legend name as a label.
However, Taylor is correct that any changes made in the Advanced dialog are not sticky. In general, I don't recommend using this option except to make final tweaks to a chart before printing/exporting. Please use the Help:Check for Updates menu option in LEAP to get the update or download and install the full new version here: http://www.energycommunity.org/default.asp?action=40
In most circumstances the label settings (accessed from a yellow button on the right-hand side of the charts in Analysis and Results view) do keep the selected labels selected. See attached screenshot showing the labels option ringed in red.
FYI, you can also save a favorite chart, which records the labels and marker settings.
Let me know your thoughts, and I will see if I can do anything to improve this part of LEAP in a future version.
I hope this helps.
Best,
Charlie