Sonia,
I am assuming you are off the iv's, are you on any oral antibiotics by chance? Although i am always on orals when i am not on iv's ( because of my cepacia) there was a time when i wasnt. I do remember a few times when the Dr. put me on an oral or two after the iv came out as a kind of back up to complete the assault on the infection i had. Also in the past( like 12 years ago), when i went on an iv i'd feel better within a week or so and my cough would completely go away for quite some time. As time went on i started noticing that my cough would still linger even though my pft's went up and i felt great. Now a days there is no getting rid of the cough no matter how long i am on an iv and i barely ever have a time where i dont have green sputum. Sometimes its lighter, sometimes darker. I'll never understand this but, a lot of times when i am just starting to get sick my sputum is lighter, almost like a yellow green when almost all the time it is normally more of a khaki color. Its is odd for it to be lighter when i am sick rather when i am well. But i am finding out the human body does a lot of odd things.
For the record i have had many many times where i dont feel good till almost a month after i am on iv's. Once i start getting active again, and living like i normally do i start to feel better and it usually reflects in my numbers. Lately it seems it takes longer and longer for me to get my numbers back where i want them.
I dont know how many years you have been getting iv's , but it could be possible that it is just going to take you longer than it used to , to get back to baseline or above.