Why is it that lately updates installs updates multiple times?

Try re-indexing Spotlight.

Spotlight – Re-index

Hold down the option/alt key while going to the  menu. Select System Information. Under Software, see if the update shows there.

If the problem is still there, try booting into the Safe Mode using your normal account. Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer. For each disable/delete, you will need to restart if you don't do them all at once

Safe Mode - About

Safe Mode - Yosemite