Cannot say for sure what is causing your problems but I do know that whatever virus they set the flu shots up for, the shots did not work on a lot of people because the virus mutated. Mutated viruses tend to be a lot nastier than the original.
Just to let you know, in the beginning of January, my husband, his brother and his sister had flu-like stuff going on that lasted well into the end of February. Fatigue and constant coughing were their main symptoms.
Hope you get to feeling better soon.
Lindaru