Scatter plot changing my horiz axis values

I'm trying to plot a large set of data for my thesis research and am having some trouble making my scatter plot work correctly. I have 3 sets of data being plotted. For each set, I have a column of x values and a column of y values. In the original raw data, there are probably 8 columns total for each set. If there was an error for an individual point, it displayed an error code in the last column. So, I set up an "if" statement column to change the cells in my x and y columns that have corresponding errors to blank (for example =if(H3=1000,C3,"") with 1000 being a code indicating no error). When I try to plot, it replaces the x values with integers. I've tried going to "format cell" to set everything to numbers but nothing changed. If I leave the x values and just set the y cells to blank, the x axis is correct but the y cells that are blank show up as zero which is misleading. Can anybody help me to sort this out? I hope I've explained this well enough.

Thanks

It's difficult to tell without seeing some example data (uploading a dummy workbook with how your data is laid out would help immensely).

You can set your formulas to return NA() (#N/A) instead of "" and Excel 2007 will ignore that point. For display purposes, i usually either have the actual data on a hidden sheet or conditionally format #n/a to white font.