Peter, It sounds as if you've answered your own question. Her previous job was higher paid so she has now  paid too much tax for her current reduced wages. Payroll systems will automatically generate a refund in such a situation.

The refund doesn't cost you any money. It comes out of the rest of your PAYE liability to HMRC. If you don't have any other employees then you can ask HMRC for the money (get in touch with your tax office), but with such small amounts it might be better to wait till the end of the year before doing that.

 It is hard to comment on what you're seeing without more information. But basically if you give the software the same information the second time you do something it will come back with the same answer as it did the first time.

But people's pay and tax won't be the same every week. In the case you originally cited they might well get a tax refund the first week (or for the first couple of weeks), but just not pay tax thereafter. If in doubt you can always use the HMRC calculator (linked to in the sticky "Why is my tax wrong?" thread at the top of this forum section). If you give that calculator the same information as you give 12Pay you will always get the same answer from both.

Thank you for buying the Premium Edition.

Going from the trial version to the premium version would have zero influence on tax calculated. It is the same software in both cases, just with premium features unlocked. You don't even re-install anything at that point. 

It is hard to guess exactly what you thought you saw happening without talking you through the forms or having a backup of your data sent to us.

Anyway, I'm glad everything is working how you expect it now.