It’s a real pain to keep all filenames in the correct case. I for myself have defined to use only lowercase filenames in my projects. When uploading files from windows to linux, all filenames are converted into lowercase by the ftp program.
Is it possible, that you can change all the filenames into lowercase in piwik?
Sorry, but this is a problem with your ftp program. Find a client with a “Don’t convert” option.
Piwik depends on a number of third party libraries which use mixed case filenames. Renaming these to lower case and changing all the includes and autoloaders would be a software maintenance nightmare.