Actually there are two accounting treatement for Indirect tax adopted by organistaions
1) Service tax collected will be Credited to Profit and Loss account and Service tax paid on Input services and amount paid to CBEC will be Debited to profit and loss account
2) Service tax collected will be treated as Liablility under head "Service tax payable" and service tax paid on Input services debited to "Service tax receivable a/c" and cash or cheque paid to department will be debited to "Service tax payable a/c" after adjusting "Service tax receivable a/c"
In first case, you treat Indirect tax as expense and income as well, in those cases, if you fail paid those Indirect taxes by the Date of Filing of Return, Then they will be disallowed u/s.43B and will be allowed in the year in which you paid such tax to respective department.
In second case, there would be no problem at all as you recognise debit items as Asset and credit item as Liability. since no expense is recognised, Disallowance of expense u/s.43B not at all arise.
No where in sec.43B explained that such expense should be paid before Due date of filing of return. So if you file late return u/s.134(4) and paid such service tax after 139(1) then still it will be allowed provided you followed method 2.