The problem got so bad, that Treasury stopped calculating the cyclically adjusted balance while it worked on a new methodology, which was only published last year.
The most politically significant changes are to the structural balance, which will mean that only the largest "one-off" expenses get included in the structural balance.
Treasury has proposed three changes.
Under the proposal, to be included in the structural balance, spending must have a "significant" impact on the government's operating balance (OBEGAL) of at least 0.5 per cent of GDP across affected years.
At the moment, this would exclude anything smaller than $1.7 billion. The spending must be "individually identifiable" in the Government's accounts, and they must clearly be one-off expenses.
A Treasury paper said the old methodology relied on "ad hoc judgements when identifying one-off items".
"This leads to inconsistent judgements over time."
The paper said that this had come to a head with the Government's Covid fund.
At the onset of the pandemic, the initial Covid support package and CRRF spending had been excluded from the structural balance.
However, the kind of spending coming out of the Covid fund changed this.
A lot of the Covid fund was spent on already-existing lines of government spending, meaning it was difficult to work out what was one-off economic stimulus, and what was a longer-term increase to a line of spending.
"... because a large quantity of CRRF spending was allocated to existing appropriations, we are no longer able to specifically identify it in the Crown accounts," the Treasury paper said.
"Further, the treatment of the CRRF at the HYEFU 2020 was inconsistent with some historic events that also had a one-off impact, such as accounting treatment revaluations,"
Spending on the Covid fund has caused headaches across Government. The Auditor–General, the Parliamentary spending watchdog, looked into the Government's Covid-19 spending, and - for a number of reasons - found it was "unable to readily or conclusively determine how much expenditure the Government has decided to approve for the Covid-19 response so far".
This was mainly due to it being difficult to disentangle Covid-related spending from ordinary spending that just happened to rise or fall in response to Covid.
The Auditor-General recommended the Government provide "regular, easy-to-access report summarising how much of the Covid-19 funding has been allocated, how much of the available funding remains unallocated, the actual amount of spending to date on main initiatives and, ultimately, what has been achieved".
Another change from Treasury is to look at the was sole parent support (SPS) benefits rise and fall with the economic cycle.
Already, Treasury forecasts and considers how much the government will spend on jobseeker benefits as the economy grows or shrinks and unemployment rises and falls.
Treasury now recognises that the number of people claiming sole parent support - designed to help struggling single parents as they look for work - rises and falls with the economic cycle.
Treasury's paper on the changes said "SPS numbers have historically shown some cyclical behaviour because sole parents have some attachment to the labour market:
"Removing these cyclical effects from the CAB and structural balance provides a more accurate picture of the government's underlying fiscal performance."