We have now discovered a slight difference between sp11 and sp10 and it revolves around the way they deal with column layouts and the use of the Base-1 feature in the column.
It would appear that if you use the base-1, base-2, base-3 etc. feature in the period column and this takes you into the prior year it will look into the prior year for the budget when the year column is set to base (previously in SP10 it did not do this and the year remained constant).
For example if you run a report for January 2010, the period column is set to base-1 and the year is base. It should go back one period which is December but as the year is set to base you would expect data in the budget column for December 2010. What we are getting is zero.
This is because the base-1 in the period is now changing the year as well and trying to display data from December 2009. As there is no data for December 2009 in this budget (yearly budget) it is returning zero.
The workaround is to hardcode the periods 1 through to 12 rather than using the base-1 functionality. We do have this logged with Microsoft at the moment, however a lot of people have just completed their year ends or are in the process of doing so, which means this issue is likely to be more obvious as people change the years in which they are processing.