Telephone Allowance - applied in last 2 payruns

I have 2 employees with a travel allowance.  Both employee's allowances have been included in their pays up until 2 weeks ago when 1 employees allowance was not included.

I did have the 2 allowances in the Standard Pay tab set up slightly differently.  One had a quanity and amount and one just had an amount but both setups seemed to be working the same.

I did recently open the employee card with the allowance set as an amount and not a quantity.  I had to update his address.  That is all that was updated.  I didn't open the Standard Pay tab at that time.

Could this have had some impace on the allowance not being processed correctly.  

Debbie