Everything seems to be fixed in v0.7. I've tested it with W3 Total Cache and it seems to be compatible.
I'm curious though, if I make a change to one of my CSS files, how does the plugin know to regenerate a new combined file? In the past, I was deactivating and reactivating the plugin through the plugin page during development -- but this is extremely cumbersome. I'm wondering, could you add a button to the WP Admin Bar at the top labeled "Re-combine CSS" so clicking it would dump the .dat file and force a new generation? And also what about just having an "Enabled" option that you can change from the admin bar to tell combine CSS whether to deliver the combined file or all the individual files as normal WP behavior? That would be killer!