I have identified that clockwork-0.62 with the option "always on top" on causes my windows to not shutdown. are they any substitutes/work arounds?? thank

Try switching to: "clockwork-0.62i" There's mention of a shutdown bug being fixed in it... not your's specifically, but might be related.

Otherwise, hook it in to a label and have the label alwaysontop.

>>> There's mention of a shutdown bug being fixed in it...

????
unsure about it... really...

Woops... it was in the non "i" version. And I guess you would know, since you did it. :D I rechecked, my mistake.