Dear Ritu,
Kindly let me know one thing are you sure have copied Custom wage types from there respective model wage type..?
If it is't check model wage type Processing classes & cumulation classes whether it's same is being assigned or not with your Cumstom wage type Like
Custom Basic wage type 1000 == Model wage type MB10
Custom HRA wage type 1001 == Model wage type M230
Custom Uniform wage type 1002 == Model wage type M200 .....!
