After a day struggling with graphs in PDFs I finally got it working. I imagine its not the sort of fix most of you would pick, but it fixed my problem and may hep someone else.
I switched to jpgraph and uploaded it to a different server(for some reason I couldnt get it working on my the same server as dompdf). I put the graph making code in a file on the jpgraph server and called the file graphmaker.php. I summoned graphmaker.php in the html that makes the dompdf pdf.
<img style="padding-left:60px;" src="http://mydomain.com/chart/jpgraph/graphmaker.php?a='.$prog1.'&b='.$prog2.'&c='.$prog3.'&d='.$prog4.'&e='.$prog5.'&f='.$prog6.'&g='.$prog7.'&h='.$prog8.'&i='.$prog9.'&j='.$prog10.'&k='.$prog11.'&aa='.$well1.'&bb='.$well2.'&cc='.$well3.'&dd='.$well4.'&ee='.$well5.'&ff='.$well6.'&gg='.$well7.'&hh='.$well8.'&ii='.$well9.'&jj='.$well10.'&kk='.$well11.'">
The crazy bit on the end is an array of two sets of variables to draw my line graphs with.
In graphmaker.php the first thing I did was parse the URL:
$url="http://".$_SERVER['HTTP_HOST'].$_SERVER['REQUEST_URI'];
$parsedurl = parse_url($url, PHP_URL_QUERY);
parse_str($parsedurl);
Parsing the URL gave me $a, $b, $c, etc variables which are storing the line graph info the graph needed.