Yes, its probably what you said above.
Do you mean youve paid some of your SEISS grant back to HMRC as an estimate of the tax on it? If you make a payment to your self assessment it will just go againat the next charge.
Also, when did you reduce your July Paymemt on account? Becuase if you did after paying January in full then some of the money you paid in January may be too much and gone aginast the 2nd Payment on account e.g if you weree due to pay £2000 tax for 19/20 in January, then there would payments on account of £1000 for 20/21 due January and July. So would have £3000 to pay in January and £1000 in July.
If later you you thought you were only going to owe 1500 for 20/21, then both payments on account become £750. So only £2750 would have been due in January. But if youd already paid £3000, then then the credit of £250 would go against July payment, so there would £750 due but onlt £500 payable.
If you log in to your account and look at the statements it should show what charges any payment have gone against.