It doesn't seem to be possible to restrict the POP3 client to read just the messages in Inbox. The POP3 protocol lacks capabilities to do that and we are not aware of any extension in GMail's POP3 protocol implementation that would enable this.
In GMail account settings, you can choose between "Enable POP for all mail" and "Enable POP for mail that arrives from now on", but this is almost certainly something else.
However, why not simply use the IMAP protocol to access GMail instead of POP3? IMAP is a more powerful protocol that understands multiple folders, so it is quite likely it won't suffer from the problem you describe.