Dear Sitaram,
It is my personal opinion to you,
(Suppose you incorporate company with 1 Lac Authorised & 1 Lac Paid Up, Then you filed form 5, from 1 Lac to 50 Lac, in this form you wrongly entered the paid up 10 lac. Now there is paid up difference of 9 Lac, right.
Now you want to make allotment with full amount of authorised capital).
In this case you file form PAS 3 for amount 9 lac in back date i.e. which is date of increase in authorised share capital , Hence, your Paid up will match.
Then after approving this form, you file another PAS 3 for remaining amount,
Hence you can solve your problem.