DiffMerge (or any diffing tool for that matter) is good if your files have a similar layout but if they are very different (like I expect your CSS might be) the might easily show the entire file as being one big difference and so prove to be no use at all.
What I would do in this situation is install the dom inspector in FireFox, and the inspect this add on.
Then, include your 2nd style sheet and view the page.
Right click on the bocked element and "Inspect this". Then change the view mode of the dom inspector to CSS. It will show you the current cascade of styles applied to the current element and also give reference to which file and which line.
This way you can figure out where you have conflicting styles.
This is admittedly no automatic process but unless your styles are 99% identical then diffing isn't going to work.