Now using Gnumeric 1.10.13 on the Ubuntu Natty Alpha 3 release on the Asus eeePC 1005ha. This bug happened 16-03-2011.

I was using Gnumeric 1.10.08 on maverick and was having similar problems (all X variable data was deleted but the Y was kept and chart formatting was lost)

When making charts with: an inverted Y-axis, deleted backplane, high positioned x-axis and labelled axes, after closing and reopening (after saving multiple during the document editting and before closing) upon reopening all this formatting was lost. I was also plotting 2 sets of data but they have been unaffected in gnumeric 1.10.13

Cell ranges were retained for both variable data sets (this was not the case when using 1.10.08) but all of my chart formatting was gone. The charts were back to their default appearance with a grey backplane, the x and y axes in the typical bottom and left positions, respectively, and axis titles were lost. 

My system is currently very up to date, I sudo apt-get update and upgraded a few hours ago. When I tested gnumeric two or three days ago to see if this problem was still there it seemed to work fine when I opened a file, reformatted a few graphs, saved, closed, and reopened the file my graphs still had the inverted y-axis, high positioned x-axis, and no backplane. 

I am available for more questions though that is about it. I really like gnumeric compared to other spreadsheets and I am dreading to have to use OO for the generation of my 90 graphs. My email is: jdunic+bugzilla@gmail.com