Is There Any Difference Between OS Installed From Disc vs A Clone Copy?

Does it make any difference to the computer? Is installing a system from a disc onto your HD any different than if its copied from a cloned backup?
IOW, does one possibly run better, or is less problem prone, than the other?

Thanks.
I ask because I did a completely new install of SL and all the apple apps I have. Then I made a clone with Superduper.
Then I went and did another application install which takes about 11 hours to do and turned out very unstable (no thanks to the maufacturer)
So, I want to go back to my previous clone (although I should check and see if those suite of apps have uninstallers) and I just wanted to know if a clone copied back is just as blessed as a direct install

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Is There Any Difference Between OS Installed From Disc vs A Clone Copy?

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