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I had a case where I had some JavaScript embedded in the <head> section and a for loop in there had a less-than sign misinterpreted as if it was the start of an XHTML tag. The code looked something like this: for (i = 1; i < 26; i++) { do stuff... } The "i < 26" was flagged as a bad XHTML tag. I either ignored it or put it in an external .js file so it would do only JavaScript syntax checking.
*** This bug has been marked as a duplicate of bug 152042 ***