Hi Varun,
For such kind of issue, the analysis steps should be something like following,
1) Whether there is any inconsistency
2) Whether it is a display issue.
For item 1, please run report SAPF190 and RFINDEX for classic. And TFC_COMPARE_VZ for new GL.
For item 2, please attach the screen shot for FBL5N and FS10N for classic or FAGLL03 and FAGLB03 for new GL for further analysis. If possible, please drill down to details.
Pls also review attached notes for help
1885677 http://service.sap.com/sap/support/notes/1885677
1885760 http://service.sap.com/sap/support/notes/1885760
1886315 http://service.sap.com/sap/support/notes/1886315
br,
Gavin