Hello,
Thank you all for your suggestions and feedback.
I have resolved the issue. For others who may want to know what I did:
Initially when I inserted the employee group in the system, I removed the old settings and inserted the new setting, this is what I believe I did wrong.
Now what I did is along with the new GL account and employee grouping setting, I inserted the old GL accounts and employee group setting (Blank Emp Grp) where it does not apply in old scenarios and it went find.
Thank you once again for your help.
Ahmed.