If there isn't any debt there cannot be interest due and as you say, HMRC charging it achieves nothing but worry for the client. It's not like the rest of their systems are functioning perfectly.
Anyway, reassure yourself by double checking the software settings - do the calculation manually if it makes you feel better and why not try Payroo helpline if you've not done so already.
Perhaps the Revenue only meant you'd have to apply for the Employment Allowance through Basic Tools if you couldn't get the commercial software to work.
I had to send an EPS to 'apply' for the Employment Allowance for all my clients. The various payroll software's that I use all did that automatically when I clicked the box to say they wanted to use the EA.
I have to say that it was more obvious in some of the software (Sage) that this was happening, whereas in 12pay I didn't realise that it had happened until I looked in the saved file.
Don't know if that helps - but may be worth checking to see if Payroo has sent the EPS?
I think with Moneysoft Payroll when you open a new file for 2014-15 it asks you if you qualify for EA. And then you have to send an EPS.
With Sage you have to tick a box and it will automatically send an EPS. Make sure you do this before you start processing any wages otherwise any weeks you have done before this will not be included in their reports.
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