Resume should work fine. I just tested it.
/splay "path\song.mp3"
Waited about 15 seconds...
/splay pause
Song stopped...
/splay resume
Song resumed from where it was stopped. Can you start by verifying that this works without using your script or queuing songs? Once we verify that it works manually without a queue, you can test it manually by queuing one extra song and manually pause/resume and see if works. That should give you a good idea of whether or not it has anything to do with your queue. Once we have that information, we can more easily look at what might be the problem. If necessary, you can always queue files without using /splay's queue.
If you're planning on using a queue, it may also be worthwhile to make your queue compatible with commonly used playlist formats so a user can insert a playlist created for something else (e.g. Winamp) and play it from your script. I did that a long time ago with 2 or 3 (I forget) different playlist formats as well as my own custom format and it worked really well. Just a thought.
