DOCTYPE Override in effect!

I recently inherited our website created in DW HTML 4.01.  I changed it to XHTML 1.0 Transitional.  When I validate each page using WC3, I get the following Warning for every page:
The following notes and warnings highlight missing or conflicting information which caused the validator to perform some guesswork prior to validation. If the guess or fallback is incorrect, it could make validation results entirely incoherent. It is highly recommended to check these potential issues, and, if necessary, fix them and re-validate the document.
DOCTYPE Override in effect!
The detected DOCTYPE Declaration       "<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">" has been       suppressed and the DOCTYPE for       "XHTML 1.0 Transitional" inserted instead,       but even if no errors are shown below the document will not be Valid       until you update it to reflect this new DOCTYPE.
Here is the code from top of all pages in my site:  Please tell me if this code is valid or what if any changes I need to make.  I am just learning HTML.  Thanks.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<title>
Also, WC3 has an option "Clean up Markup with HTML Tidy."  What is this?  Can I click this to clean up my code?  Can I use this confidently if I know so little HTML?  Thanks again.

>I recently inherited our website created in DW HTML 4.01.
>I changed it to XHTML 1.0 Transitional.
You mean you changed just the doctype, or you changed both the doctype and all of the code on that page too?

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