It sounds like the timer being stored is not storing the same command that is run when the Pc is on.
It sounds like with the Pc running, timers and macros (even those stored in the interface) get run from the PC. (I can't verify that, but that's what it sounds like to me at least).
You said that the Activity Monitor shows the correct "on" command for the lights.
What is the EXACT command you see (is it a "Bright 100," an "Extended Dim," or an "On" command?
What about when you manually turn on the light via the AHP interface?
AHP cannot capture any events if the PC is off, so it is understandable that you won't see anything in the AHP event logs for the time the PC was turned off.
However, the X10nets service should be running as a background service, even when AHP is not open. As long as it is running (with the unit attached of course), it will try to capture those events.
When you shut the PC down, are you disconnecting the serial cable from the CM11A? I remember reading something a number of years ago about the CM11A not running timer and macros correctly if the cable was left attached, but the PC was shut down. You might try unplugging the cable (and for some reason it seemed to make a difference if you unplugged the CM11A-end of the cable or if you unplugged the PC-end), and seeing if there is any difference.
Also, please confirm that timers for BOTH the SoftStart AND the Non-softStart modules are the ones that are not turning on.
I suspect the CM11A might not be properly storing the Extended Dim commands, while it storing the "simple" commands (on/off) just fine.