I don't know if save as PDF is related to excel 2003 or not, but it seems like excel 2003 doesn't have the functionality that we're using. Formatting Rule "Use a forumula to determine which cells to format" seems to be a 2007 only functionality. Excel 2003 is more limited in what it can do conditional formatting wise.
Yes, Excel 2007/2010 (XLSX file format etc.) provides more advanced conditional formatting types than Excel 97-2003 (XLS) which has limited support for conditional formattings.
Regarding your issue of PDF rendering (i.e., conditional formatting rules are not applied in the rendered PDF by Aspose.Cells), could you specify FileFormat type as XLSX if you are creating the spreadsheet from the scratch to render PDF file format.
See the sample line of code below:
Workbook workbook = new Workbook(FileFormatType.Xlsx);
If you still could not evaluate, kindly do provide us a sample console application (runnable), zip it and post it here to show the issue on our end. We will check your issue soon.