RTI file sent correctly but HMRC records not correct - how do I fix this?

The Month 2 submission was sent correctly to HMRC - I checked the submission file data and it was correct. But the HMRC records for Month 2 show the YTD PAYE for 1 employee as the monthly deduction. Have submitted further months but this has not corrected. The software company cannot do anything and HMRC cannot resolve it. How do I fix this? It is a data corruption/mapping error int he HMRC records. AS PAYE is paid via direct debit HMRC have taken too much money.

Hi ,
 

If everything has been sent correctly from your end and the payroll software accurately reflects this but HMRC are holding incorrect liability totals, please contact our Employers Helpline on 0300 200 3200 where we will compare the totals and raise a "disputed charge referral" if required. We will also need to access your record and send a refferal regarding the incorrect payment being taken.  Thank you .