[Plugin: WP Super Cache] Permalinks and Rejected URLs conflict

Hi,
Recently, I’ve updated WP Super Cache and with the new update it refused to work with the default permalink structures. In the previous version it was working fine.

Anyway, I changed my permalink structure and since I am on a Windows shared server, there’s an “index.php” string in the middle of my permalinks.
Although the home page is being cached fine, the posts and pages which include index.php string in the permalink are not cached.

The problem is because of the rejected “index\.php” string which is stated in the rejected strings list by default.
If I delete this string, it works. But I don’t know the function of that string. My questions are:

-What is the function of rejecting “index\.php” string?
-Is it OK if I remove that string from the list?
-Is there an alternative string for the same task that won’t conflict with the permalinks containing index.php string?

Thanks,
Demir
P.S. I selected “Use PHP to serve cache files.”