Can I avoid the Israel-Syria visa problem by using different pports?

I was planning on using one pport for Israel and Jordan, then my second pport (dual citizen) for Syria which would have no Jordanian or Israeli stamps. But if I can�t get a Syrian visa at the Syrian border then I�d have to apply in Jordan, in which case the Syrian emby at Amman might wonder why my second pport doesn�t even have a Jordanian visa in it and then might refuse to grant any visa at all?