Sounds like a regular type of phobia (and the less phobia feeling after exercising can be due to an increase in seratonin "the happy hormone" caused by exercise which can change your brain function, though you are very perceptive to have noticed this).
Have you tried Emotional Freedom Techniques (EFT)?
You can download a free manual describing how to do it for yourself from the eft universe...
Get Started Free
... though many people find going to a practitioner more beneficial as the practitioner can look out for those signs of 'denial' etc. and work with you and support you in treating it.
EFT, whilst it may seem a very odd technique when you read about it, is especially good for phobias. I used to have a bad phobia of spiders and when I went to learn EFT (long story as to why I did, won't bore you with it), when we practiced it on the course, I decided to treat my phobia. Bam! it was instantly gone, and I just knew it, though it was a really odd feeling as I couldn't get the fear to arise any more nomatter how much I tried (and it had been easy enough beforehand, just from thinking about it). That's when I knew that EFT really worked.
There are other techniques that can help too, such as hypnotherapy, NLP, timeline therapy, Freeway CER (which is similar in some ways to EFT) etc., but EFT is one of those that is freely available to learn (there are even people demonstrating it on youtube) and there are practitioners of it worldwide, so there's bound to be one fairly local to you.
Hope that helps. If you have any questions, feel free to ask.
Hugs
Giles