That looks right... you would want to add the increment code just after the opening "do" tag like this:
<?php do { ?>
<?php ++$incnumber; ?>
<tr class="<?php echo $WARRT_AltClass1->getClass(true); ?>">
<td class="WADAResultsTableCell"><?php echo $row_WADAloadingDock['submitTime']; ?></td>
<td class="WADAResultsTableCell"><?php echo($row_WADAloadingDock['fileName']); ?></td>
<td width="90" align="right" class="WADAResultsTableCell">
<form id="form1" name="form1" enctype="multipart/form-data" method="post" action="">
<?php
WA_DFP_SetupDownloadStatusStruct("WA_DownloadResul t1");
if(isset($_POST["'download'.$incnumber"])){
WA_DFP_DownloadFile("WA_DownloadResult1", "uploads", "".$row_WADAloadingDock['fileName'] ."", "[FileName]", false, false, false, "", "", "", "");
}
?>
<input type="submit" name="download<?php echo $incnumber; ?>" id="download<?php echo $incnumber; ?>" value="Download" />
</form>
</td>
</tr>
<?php } while ($row_WADAloadingDock = mysql_fetch_assoc($WADAloadingDock)); ?>