I cannot find the difference between these wp_capabilities values in wp_usermeta

You’ve posted some serialized arrays.

The first entry, a:1:{s:13:"administrator";s:1;} is corrupted – that’s not a valid serialized array.

The second entry, a:1:{s:13:"administrator";s:1:"1";} looks like this when unserialized:

array (
  'administrator' => '1',
)

The third entry, a:1:{s:13:"administrator";b:1;} looks like this when unserialized:

array (
  'administrator' => true,
)

In my setup, capabilities are stored like your third example, a:1:{s:13:"administrator";b:1;}. The underlying cause of your issue is probably related to the code that deals with how the user capabilities are being stored.