[eluser]ejangi[/eluser]
I've had this issue a few times... I'm assuming you're using the PHP Eclipse plugin/editor? I've found that if I try to put an HTML comment into the editor it locks up just before I put the second dash in (i.e. "<!-") and if I close the editor and try to re-open the file I get the error you described.
I'm not sure if that's the problem you're having, but I thought it was worth mentioning. You may need to find and post on the PHPEclipse forums to get further help. Best of luck!