Graphic conversion from 3.5 to 4.4.2

I converted a site from FY 3.5 to FY 4Pro. The site has numerous flowcharts with horizontal and vertical arrows. All the flowchart objects, including the arrows, are .gif and are layers. All objects view okay on browsers IE, Firefox, Safari and Preview except the vertical arrows. They appear to be positioned on the page at random.
Has anyone experienced a similar problem when converting from FY 3.5 to FY 4Pro and if so, how was it corrected?

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