Currently, when I open multiple spreadsheets, they open in different
instances of excel. As a result (i believe), I cannot paste special values (
in the way they would if they were in the same instance). I have tried
checking and unchecking "ignore other applications", "windows in taskbar".

I use the transpose, format, etc quite often. I recently had Excel 2003 and
2007 installed on the same computer. This issue arose when i removed 2007.
Since then, I have reinstalled 2003, but the problem still persists.