Hi Ben,
Thank you for the update.
I am afraid that I was not able to reproduce the issue. Also I have created a simple sample and it is available in the below link:
http://websamples.syncfusion.com/samples/XlsIO.Windows/69361/main.htmIn the above sample I have read conditional format from existing template and modified the formula using XlsIO and the formula in the cell A1 is modified.
Please have a look at the above sample and if still the issue exists, could you please try reproducing it in the above sample and send us the modified sample so that we could sort out the cause of the issue and provide you a solution?
Thanks,
Melba