When you install SQL 2008 R2 workstation components you get a newer version of BIDS (BI Developer Studio, included in the workstation components) that replaces BIDS 2008 version (BIDS 2005 still live side-by-side). Everything would be good if you can use the newer version to edit any 2008 AND 2008R2 project.
SSIS editor doesn’t offer a way to set the “compatibility level” of the package, becuase it is almost all unchanged. However, if a package has an ADO.NET Destination Adapter, there is a difference in XML format that requires some manual changes to move a SSIS project back and forth between BIDS 2008 and BIDS 2008R2.
John Welch wrote a very good post about this issue, explaining how to make the changes if you need to.