I get different results when I run a YTD class report from Reports menu versus doing Lists, Classes, Run Report. In particular, income from Journal entries yields different and opposite results in these two types of reports.
Running a transaction list from the Reports -> Budget report shows the correct result, whereas running a Report from the Lists -> Classes -> Run Report method shows these Journal entries as opposite results.
It sounds to me like the Budget Report is looking at the transactions from a Debit perspective and the List report is looking at it from a Credit perspective. Either way, you get the same values, correct? Only one is negative and the other positive? If the Budget Report is correct for you, why not use it? Is there some functionality it's missing?