I may be wrong, but negatives are not supposed to be touching the glass on the Epson 4990. That's one of the reasons for the Epson holders.
To that end, Doug Fisher has created an entire series of holders that can be adjusted to achieve best focus, since there is some variability among individual scanners.
See www.BetterScanning.com for what he calls the Variable Height Mounting Station.
The "before and after" example shown here, may strike a familiar chord.
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