Natalie...it really depends on what feelings these dreams that contain your ex evince. Tell us what happens in some of these dreams and it will become more clear.
Right away you should write the dreams down - then think about your Ex and write down all his character traits - well, the first few that spring to mind immediately.
It could be your relationship to your own Inner Male (Animus) that is causing some problems. If I have a little time I could look up your astrological chart and check out the shape of your Mars (that will tell us how healthy this Inner Male is....Mars symbolizes Doing Energy - where you put your energy to get what you want. Venus, on the other hand, shows you WHAT you want - your Values)
By the sounds of it (you having MCS etc) it sounds like your Mars needs some healing (your dreams of your Ex may be sounding this alert - it will be interesting to see what Character Traits you come up for him! HIS character traits are a reflection of YOUR Inner Male!).
If you give me your birthday, don't forget your Time and place of birth either.
Awareness if the first step to healing and I think you're on your way! (the fact that you intuitively feel there is something to these dreams with your Ex is meaningful)