I'm not completely certain what you want the result to be, but I think this code does something like what you're looking for:

$line = '';
while (<FH>) {
  chomp;
  if (length) {
    $line .= "$_ ";
  } else {
    print <<"EOHTML";
<TR>
  <TD>Checkbox</TD>
  <TD>$line</TD>
</TR>
<TR bgcolor=#000066><TD WIDTH=298>&nbsp;</TD><TD WIDTH=298>&nbsp;</TD>
+</TR>
EOHTML
    $line = '';
  }
}
if (length $line) {
  print <<"EOHTML";
<TR>
  <TD>Checkbox</TD>
  <TD>$line</TD>
</TR>
EOHTML
}
[download]

Note that I replaced the regex with a call to length. I think this is a clearer way to check whether the line contained any text (after chomping, of course).

Your question would be clearer with sample input and output...