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Here is a simple example:

Manipulate[Plot[Sin[2 Pi f t], {t, 0, 10}], {f, 0, 5}]

This makes a plot with a sine wave of varying frequency determined by f. Go to the File->CDF Export->Standalone menu item and save as a .cdf file (I called mine test.cdf). Now open test.cdf in the Wolfram reader and the Manipulate is colored pink and presents an error message "An unrecognized option name UndoTrackedVariables was encountered". The Manipulate appears to function, but it is quite disconcerting to see the pink error-color on the Manipulate.

My questions are: can anyone reproduce this (I'm using version 10.0.1 on Mac OS 10.9.5)? Second, can anyone think of a way to remove the error message and get the cdf's back to normal? Thanks!

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This issue is due to the fact, that the stand alone CDF Player is still in version 9.
Opening the cdf file in a browser with a Mathematica 10 plugin installed works without any problem. Also creating the cdf file with version 9 works properly.
If you need to make this cdf work in the version 9 player and want to use Mathematica version 10 to create it, you can do the following:

cdf = Import["D:\\test.cdf"];
Delete[cdf, Most@Flatten@Position[cdf, UndoTrackedVariables]];
Export["D:\\test_v9.cdf", %]

This will just delete the UndoTrackedVariables entry that is causing the incompatibility.

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    $\begingroup$ Thanks Karsten -- the workaround is good, though my notebook actually has 2 Manipulates in it. In this case you can replace the middle line with Delete[cdf, Most /@ Position[cdf, UndoTrackedVariables]]; and it Deletes both the UndoTrackedVariables. $\endgroup$ – bill s Sep 19 '14 at 23:59

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