This is not a problem. In fact, with Version 2010, you have a new and different Report that hasn't been in previous versions of Family Tree Maker.
I hope that you are using the Family Group Sheets for your folders. You could use the FGS for the folder for each family.
The New feature is the Individual Report, or Person Reports, selecting the Individual Report. You can print that for your filing system.
If find that this report is helpful when doing some research for an individual, when I am not in Family Tree Maker doing the research.
RE: Scotts / Macdonald issue:
Just so that I understand, and I do remember us talking about that. But, since it is still an issue, lets address it.
Do you have these two "lines" in the SAME Family Tree Maker file?
You said that you successfully attached via FTM. But did you Merge two files or are both lines in the SAME Family File?
This gets back to Files vs Trees.
You could have had the Scott TREE and the Macdonald TREE is two separate Family Files, or you could have had both Trees in the SAME Family File.
It they were in two Family Files, you can Merge them.
What you have to do, to see both the Scotts and Macdonalds in a Tree, is to go back to the Common Ancestor before you will see that Branch in a Genealogy Report. (starting with the common Ancestor) It's easier to see the two "trees" by creating looking at Descendants of that Ancestor. If you look at the Outline Descendant Report, you will see a [#] in front of the multiple relationships that happen when Cousins Marry.
When you saw the Extended Family Chart, were the Scots and Macdonalds lines connected? or were they two different trees / branches.