Yes, it is exactly the same version (only one) on the same computer!
It just the way to call it that is different: from php or from a cmd prompt.
The exact error message is:
“SQLyog Job Agent Version 4.1
Copyright © Webyog Softworks Pvt. Ltd.. All Rights Reserved.
This version of SJA has expired. To register SJA you need to purchase SQLyog from…”
I obtained this message during the trial period (before the end) and also after purchasing the license.
Since only the environment from where the command is called is different, since the program is found (it replies with the error message), I could just imagine that the problem is linked with the “path” to the licens. Strange.
Everything is the latest: XP SP1, PhP 5, Apache 2…
Everything else works fine (especially other system commands).