Hi Saurabh,
I am afraid that I am not able to reproduce the issue that you have mentioned here. Please refer the following steps that I tried to reproduce it:
1. Created simple sample with GGC.
2. Applied custom css for columnHeaders and GroupCaptionCell
3. The styles were applied properly to both the cells.
Please refer the sample from the below link, which illustrates this:
http://websamples.syncfusion.com/samples/Grid.Web/6.4.0.15/GGC_Web_CustomCSSGroupCaption/main.htmPlease have a look at the above, and try like this, if still the issue exists, could you please reproduce it with the above sample, and send back to us. So that we could sort out eh cause of the issue very soon and provide you a better solution.
Regards,
Raji