I believe this happens when Office 2010 is installed natively and Office 2003 ThinApp is registered/installed on the same machine.
When doing so, the Office 2003 filetypes (eg .xls) will overwrite the Office 2010 filetypes.
You can edit the package.ini of Office 2003, look for the below section and remove those filetypes that you want to use Office 2010.
[Microsoft Office Excel 2003.exe]
Source=%ProgramFilesDir%\Microsoft Office\OFFICE11\EXCEL.EXE
Shortcut=Microsoft Office 2003.dat
FileTypes=.csv.dif.dqy.iqy.oqy.rqy.slk.xla.xlb.xlc.xlk.xll.xlm.xls.xlshtml.xlt.xlthtml.xlw
Comment=Perform calculations, analyze information, and manage lists in spreadsheets or Web pages by using Microsoft Office Excel.
ObjectTypes=Excel.Addin;Excel.Application;Excel.Application.11;Excel.Backup;Excel.Chart;Excel.Chart.8;Excel.CSV;Excel.Dialog;Excel.DIF;Excel.Macrosheet;Excel.Sheet;Excel.Sheet.8;Excel.SLK;Excel.Template;Excel.VBAModule;Excel.Workspace;Excel.XLL
Shortcuts=%Programs%\Microsoft Office
Now, rebuild the ThinApp by running build.bat and try if it helps.