HMRC tax penalty effect on Tier 2 Dependent Visa

Hi,
My wife was working as a self employed for about a year and then we left UK (may 2014). She filed the tax on time (for 2012-13 and 2013/14) and told HMRC that she has stopped working. We got to know that she still has to pay the tax and they cannot cancel the tax for the year 2014/15 as it is too late. We filed the tax return anyways now with zero earnings and stating that she was not employed in this period.

Now we are going to write HMRC to waive off the penalty of 1600 pounds.

Is there any effect on the tier 2 visa application for this penalty as we will be applying for this very soon?

Update:
HMRC has waived off all the penalties and closed the account. Can anyone tell me if we need to write this in the visa application form?

Jibran