Rewrite rules missing when membership is active

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 Membership plug in.

So, when membership is deactivated all custom post rules are working. When membership is active, they are showing as missing. This includes a lot of things, like password resets, user profile information, portfolio and attachments.

Here are the rules affected by membership 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?