Puh. no special characters, nothing suspicious…
The client log should have a warning for each clash, in the form of "Detected case clash between" << file << "and" << realFileName;
When we see the clashing pair, maybe that gives a hint.
Press CTRL-L on the settings window to open the log output dialog.
Can you make a simple test to check that you filesystem is really case insensitive?
You would need to put windows in to case-sensetive mode. AFAIK there is no possibility to do this. The linux server should already be case-sensitive by default