These 3 lines are definitely not coming from ShopSite generate code since ShopSite doesn't do any xhtml code in the templates.
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/HEAD><!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" dir="ltr" lang="en-US">
<head profile="http://gmpg.org/xfn/11">
ShopSite does output this code
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<meta name="generator" content="ShopSite Pro 10 r7.4 (data - template-name">
1 Places you can check for those lines of code would be the Page Header under Preferences > Header/Footer (or Preferences > Layout Settings > Header)
2 The template that is used by the pages. There may be and [-- IF ... --] statement that is being executed or excluded depending on a field in the page data,
3 Any of the Page Text fields , Text 1, Text 2, Text 3 on the Edit Page Info screen for the page.
4 If the pages that have the extra code are product more-information pages then the code could be from the [-- DEFINE MORE_INFO_PAGE --] section of the product template.
5 Are the pages actually being generated by ShopSite? Maybe the pages were created manually or were created in ShopSite but the filename was changed so ShopSite isn't actually modifying them any more. You can test this by editing something on the page and then seeing if the page is updated with that information after you do a Utilities >Publish > Regenerate.
If you have just a few pages defined it won't be much of a problem to search the page fields such as text 1, 2, 3 for some of that text . I would do this by going to the Edit Page Info screen of the products and in the browser do Ctrl-F which will open a search box in the browser window. Type something that is in one of the 3 lines above like "xhtml" (without the quotes and see if it is found on any fields. If it is then you should remove the lines that shouldn't be on the page.
If you have a lot of pages it may be easier to download the pages in tab delimited format (Utilities > Database > Download >Pages ) and then open the file in Excell or another spreadsheet application and do the same type of search to see if the text is found in any fields.
Looking in the templates would be done under Merchandising> Custom Templates the Pages or Products > then Edit the template file and do a similar Ctrl-F search.
A link to the pages that are having problems may be helpful so we an see the actual code that is different on the pages.