Rewrite Rules not working due to classifieds

More and more parts of the website are becoming unavailable delivering 404's.

Finally on loading the rewrite rules inspector plug in, we found that there are scores of rules missing. On deactivating all plug ins and slowly reactivating them one by one, checking the rewrite rules each time - it seems that it is being caused by the Classifieds plug in.

If we deactivate or remove the plug in - everything gets even more screwed up. If we leave it active - loads of rewrite rules (such as password resets) are not working.

So, when classifieds is deactivated all custom post rules are working but loads of things are redirecting to the wrong place.

When classifieds is active, the redirect problem disappears but the following rewrite rules show as missing - password resets, user profile information, portfolio and attachments.

Here are the rules affected by classifieds being active:
(.?.+?)/add-payment-method(/(.*))?/?$ index.php?pagename=$matches[1]&add-payment-method=$matches[3] missing
(.?.+?)/customer-logout(/(.*))?/?$ index.php?pagename=$matches[1]&customer-logout=$matches[3] missing
(.?.+?)/lost-password(/(.*))?/?$ index.php?pagename=$matches[1]&lost-password=$matches[3] missing
(.?.+?)/edit-address(/(.*))?/?$ index.php?pagename=$matches[1]&edit-address=$matches[3] missing
(.?.+?)/edit-account(/(.*))?/?$ index.php?pagename=$matches[1]&edit-account=$matches[3] missing
(.?.+?)/view-order(/(.*))?/?$ index.php?pagename=$matches[1]&view-order=$matches[3] missing
(.?.+?)/order-received(/(.*))?/?$ index.php?pagename=$matches[1]&order-received=$matches[3] missing
(.?.+?)/order-pay(/(.*))?/?$ index.php?pagename=$matches[1]&order-pay=$matches[3] missing
members-home/documentation/[^/]+/([^/]+)/comment-page-([0-9]{1,})/?$ index.php?attachment=$matches[1]&cpage=$matches[2] missing
members-home/documentation/[^/]+/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/documentation/[^/]+/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/documentation/[^/]+/([^/]+)/trackback/?$ index.php?attachment=$matches[1]&tb=1 missing
members-home/documentation/[^/]+/([^/]+)/?$ index.php?attachment=$matches[1] missing
members-home/documentation/([^/]+)(/[0-9]+)?/?$ index.php?documentation=$matches[1]&page=$matches[2] missing
members-home/documentation/[^/]+/attachment/([^/]+)/wc-api(/(.*))?/?$ index.php?attachment=$matches[1]&wc-api=$matches[3] missing
members-home/documentation/[^/]+/([^/]+)/wc-api(/(.*))?/?$ index.php?attachment=$matches[1]&wc-api=$matches[3] missing
members-home/documentation/([^/]+)/wc-api(/(.*))?/?$ index.php?documentation=$matches[1]&wc-api=$matches[3] missing
members-home/documentation/([^/]+)/comment-page-([0-9]{1,})/?$ index.php?documentation=$matches[1]&cpage=$matches[2] missing
members-home/documentation/([^/]+)/page/?([0-9]{1,})/?$ index.php?documentation=$matches[1]&paged=$matches[2] missing
members-home/documentation/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ index.php?documentation=$matches[1]&feed=$matches[2] missing
members-home/documentation/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?documentation=$matches[1]&feed=$matches[2] missing
members-home/documentation/([^/]+)/trackback/?$ index.php?documentation=$matches[1]&tb=1 missing
members-home/documentation/[^/]+/attachment/([^/]+)/comment-page-([0-9]{1,})/?$ index.php?attachment=$matches[1]&cpage=$matches[2] missing
members-home/documentation/[^/]+/attachment/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/documentation/[^/]+/attachment/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/documentation/[^/]+/attachment/([^/]+)/trackback/?$ index.php?attachment=$matches[1]&tb=1 missing
members-home/documentation/[^/]+/attachment/([^/]+)/?$ index.php?attachment=$matches[1] missing
members-home/portfolio/[^/]+/([^/]+)/comment-page-([0-9]{1,})/?$ index.php?attachment=$matches[1]&cpage=$matches[2] missing
members-home/portfolio/[^/]+/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/portfolio/[^/]+/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/portfolio/[^/]+/([^/]+)/trackback/?$ index.php?attachment=$matches[1]&tb=1 missing
members-home/portfolio/[^/]+/([^/]+)/?$ index.php?attachment=$matches[1] missing
members-home/portfolio/([^/]+)(/[0-9]+)?/?$ index.php?portfolio=$matches[1]&page=$matches[2] missing
members-home/portfolio/[^/]+/attachment/([^/]+)/wc-api(/(.*))?/?$ index.php?attachment=$matches[1]&wc-api=$matches[3] missing
members-home/portfolio/[^/]+/([^/]+)/wc-api(/(.*))?/?$ index.php?attachment=$matches[1]&wc-api=$matches[3] missing
members-home/portfolio/([^/]+)/wc-api(/(.*))?/?$ index.php?portfolio=$matches[1]&wc-api=$matches[3] missing
members-home/portfolio/([^/]+)/comment-page-([0-9]{1,})/?$ index.php?portfolio=$matches[1]&cpage=$matches[2] missing
members-home/portfolio/([^/]+)/page/?([0-9]{1,})/?$ index.php?portfolio=$matches[1]&paged=$matches[2] missing
members-home/portfolio/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ index.php?portfolio=$matches[1]&feed=$matches[2] missing
members-home/portfolio/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?portfolio=$matches[1]&feed=$matches[2] missing
members-home/portfolio/([^/]+)/trackback/?$ index.php?portfolio=$matches[1]&tb=1 missing
members-home/portfolio/[^/]+/attachment/([^/]+)/comment-page-([0-9]{1,})/?$ index.php?attachment=$matches[1]&cpage=$matches[2] missing
members-home/portfolio/[^/]+/attachment/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/portfolio/[^/]+/attachment/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?attachment=$matches[1]&feed=$matches[2] missing
members-home/portfolio/[^/]+/attachment/([^/]+)/trackback/?$ index.php?attachment=$matches[1]&tb=1 missing
members-home/portfolio/[^/]+/attachment/([^/]+)/?$ index.php?attachment=$matches[1] missing
members-home/documentation/page/([0-9]{1,})/?$ index.php?post_type=documentation&paged=$matches[1] missing
members-home/documentation/(feed|rdf|rss|rss2|atom)/?$ index.php?post_type=documentation&feed=$matches[1] missing
members-home/documentation/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?post_type=documentation&feed=$matches[1] missing
members-home/documentation/?$ index.php?post_type=documentation missing
members-home/portfolio/page/([0-9]{1,})/?$ index.php?post_type=portfolio&paged=$matches[1] missing
members-home/portfolio/(feed|rdf|rss|rss2|atom)/?$ index.php?post_type=portfolio&feed=$matches[1] missing
members-home/portfolio/feed/(feed|rdf|rss|rss2|atom)/?$ index.php?post_type=portfolio&feed=$matches[1] missing
members-home/portfolio/?$ index.php?post_type=portfolio missing
^your-profile/([^/]+)/? index.php?page_id=1672&upme_profile_filter=$matches[1] missing
^your-profile/([^/]+)? index.php?page_id=1672&upme_profile_filter=$matches[1] missing
downloads/(.+) index.php?protectedfile=$matches[1]

What is happening here? I really need all parts of the site working - how can this be fixed?