Eventually I got to speaking with the site manager and I mentioned in passing the cards. He clammed up immediately and I shrugged it off.
A few months later after I left, the manager and I were having a beer and grouching about that site and he told me that those cards were for the local .. well mafia for lack of a better word. They were clocked in by a senior member every day, and clocked out at the end, the pay cheques were sent off and as a result we never had any break ins.
Crazy.
It opened my eyes up a lot and over the years since then I have seen similar things in a few other industries, eg in Japan and hospitality we had a very friendly grandpa style gentleman visit the restaurant once a month, hand over a receipt to the manager and she paid him some cash. Turns out he was Yakuza and that was our payment for the month