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That is line 99. Here is what i would try.
For one make sure again all uploads directories are cleared and there is nothing under uploads. Next make sure you have applied the ini_set line as noted. Next make note of what size files your trying to upload. Try a 125kb or so file first and work your way up. See where you stop. Next if you have imagemagick always use that over gd2 and in your global options clear the jpegtran line.