Why are deposits turning negative on chart?

When I record a split deposit to my checking account, I put the amount in the "increase" column. This yields a positive number being recorded as a "deposit". Seems fine. But when I generate a report that includes that category, two problems occur. First, the deposit shows up on the report in the income section as a negative number (it should be a positive number). Second, the entire deposit shows up there, although only one part of the split was in this category, with the other items in the split being catgorised differently. I can't figure out what to do about this -- it makes bookkeeping impossible!