Prueba rápida:
Código PHP:
$usertable = "datosgpx";
$string_gpx = '<gpx xmlns="http://www.topografix.com/GPX/1/1" xmlns:gpxx="http://www.garmin.com/xmlschemas/GpxExtensions/v3" xmlns:wptx1="http://www.garmin.com/xmlschemas/WaypointExtension/v1" xmlns:gpxtpx="http://www.garmin.com/xmlschemas/TrackPointExtension/v1" creator="eTrex 10" version="1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.topografix.com/GPX/1/1 http://www.topografix.com/GPX/1/1/gpx.xsd http://www.garmin.com/xmlschemas/GpxExtensions/v3 http://www8.garmin.com/xmlschemas/GpxExtensionsv3.xsd http://www.garmin.com/xmlschemas/WaypointExtension/v1 http://www8.garmin.com/xmlschemas/Wa...xtensionv1.xsd http://www.garmin.com/xmlschemas/TrackPointExtension/v1 http://www.garmin.com/xmlschemas/TrackPointExtensionv1.xsd"><metadata><link href="http://www.garmin.com"><text>Garmin International</text></link><time>2014-05-23T11:25:26Z</time></metadata><wpt lat="-34.904523" lon="-54.931642"><ele>15.331123</ele><time>2014-05-23T11:25:26Z</time><name>001</name><sym>Flag, Blue</sym></wpt><wpt lat="-34.904081" lon="-54.931771"><ele>15.963099</ele><time>2014-05-23T11:34:53Z</time><name>002</name><sym>Flag, Blue</sym></wpt><wpt lat="-34.904184" lon="-54.932191"><ele>14.877506</ele><time>2014-05-23T11:40:36Z</time><name>003</name><sym>Flag, Blue</sym></wpt></gpx>';
$gpx= simplexml_load_string($string_gpx);
foreach($gpx->wpt as $wpt) {
$lat = $wpt['lat'];
$lon = $wpt['lon'];
$ele = $wpt->ele;
$fecha = $wpt->{'time'};
$query = "INSERT INTO $usertable (fecha,lat,lon,ele) VALUES ('$fecha','$lat','$lon','$ele')";
echo $query;
}
PD: Para que el xml fuera válido, te faltaba un </gpx> al final...