Got the same problem right now, found any solutions? I’m using do_shortcode(‘[put_wpgm id=1]’) etcetera in a template.php
Edit: After examining the code, it seems that both maps get the same id, id=”wgmpmap”, and this could be causing only the first map to get targeted. Any way to change the id’s of each map?
Edit2: Digging into the support posts this is apparently not supported by the lite version (even though it says “Add any number of Google maps on pages/posts/sidebars”)
Switched to the “Google Maps Ready!”-plugin and the free version worked fine with multiple maps, the UI is a bit messy though but nothing too bad.