Unfortunately, Subversion is case-sensitive. This is due to the fact that files from Subversion can be checked out on both case-sensitive file systems (e.g., *nix) and case-insensitive file systems (e.g., Windows, Mac).
This script may help you avoid problems when you check in files. If it doesn't solve your problem, my best suggestion is to write a little script to make sure that all extensions are lowercase and run it every time before you check in/check out. It'll be a PITA, but maybe your best bet.