Google treats urls with and without capital letter as unique urls.

Trying to figure out how to fix the problem I have created for myself.

[Ledfish]

I have a website that I redesigned about 6 months ago. Shortly thereafter, the interior pages would not rank as they had previously. The redesign was not major, mostly the appearence(i.e. graphics changed).

So for the last 6 months I have been banging my head against the wall trying to figure out what the heck was the problem.....Tonight I found out and now figuring out how to resolve it has turned into a really big concern. Hopefully some one will have some guidance or possibly I'll be lucky enough that Google Guy will see this post and be able to give me some help.

So heres is the problem :

Previously our internal urls looked like this:

www.mysite.com/SomeDirectory/somefile.asp

When we did the redesign all urls were referenced as:

www.mysite.com/somedirectory/somefiles.asp

Notice that the first url has capital letters in "Some Directory(BTW it also shows in google as part of the supplemental index), while the second one has "somedirectory" all in lowercase., thus creating a duplicate content penalty situation and explains why the internal pages are not ranking.

Google now lists both these urls and this is most likely causing a duplicate content penalty situation and thus explains why the internal pages are not ranking, the problem is compounded because our web server does not differentiate between urls with and without capital letters in them.

The total number of pages with "SomeDirectory" with captial letters in the url total approximately 700 so trying to manually remove them could be tough. Also I'm worried that by using the url removal tool, I might accidentally cause both pages to be removed.

Anybody have any idea what I can do?