On linux, filenames and directories are case sensitive. file and File are different files.
On Windows, filenames are not case sensitive. file and File are the same file.
MySQL saves a database to disk. A "database" is saved in a directory, and each table is saved as a file in that folder.
Thus, say you transfer a database from Linux to Windows that has a table named "userBookmarks", this might cause a problem for you because MySQL on Windows will likely interpret it as "userbookmarks".
There's a setting in your my.cnf file called "lowercasetable_names".
The options are 0, 1, and 2.
1 is the default, and you shouldn't need to change it.
If you change it to 0 on Windows, you might run into problems. If you change it to 2, it doesn't seem to do much.
So what's the solution? Try to avoid capital letters in table names (use _ instead of camel case). When you can't do that, write your code for the Linux database (ie "select from userBookmarks"), and your queries should translate fine on Windows since Windows will convert that to "select from userbookmarks".