I finally got around to fixing the auto play on start-up problem. The reason it took so long was because I was trying to perfect the auto restart option:

Sometimes when an AC3 file is played or something that takes control of the sound card SPDIFkeepAlive gets stopped. The auto restart option restarts playback every 3 seconds. This means that shortly after AC3 playback stops SPDIFKeepAlive resumes automatically.

Unfortunately I’ve still not got it working properly, at least not for me, depending on your sound card / driver you might get better results.  But be warned, on my system after a random amount of time (~1 hour) I get a terrible noise produced by SpdifKeepAlive and I have to exit, hence I don’t use this feature! I’ll try to fix it sometime. I think I’ll need to use threading and play 2 files that continuously overlap.

You can download the new version at the bottom of the SPDIFKeepAlive Post