From the help of the main program I'm havining issues with. Also have issues with Samurize, but that's more random.
Start Option may solve some troubles you faced.
Right-click the shortcut of ThroughClock and show the properties. Type the option below one space after the file name in the Target window.
Options you can set are,
/wait:seconds
Use this option in case the Clock appears at different position from previous session. "Seconds" must be typed the number between 0 to 999. The Clock may wait for those seconds to start. 5 to 20 would generally be good to solve your trouble.
/fpu
When you faced an error message about FPU, this option command initializes it and will avoid the trouble.
/ns
This makes the Clock on Windows95 not use Screen Saver Manager.
Start Options do not differ uppercase or lowercase. You can set plural options together with.