I need help with Achilles Tendinitis

I developed AT about three months ago.  It just happened to show up one day out of the blue near the end of a long run.  Once I felt this, I slowed down, got home and iced it.  Since then it has shown up at the beginning of my runs then goes away.   Occassionally it will show up again after I finish my run, but rarely.  After a month (7) PT sessions, I feel like I am making progress.  My PT is a triathlete and excellent runner so she knows her stuff.  She seems to think it is from tight muscles.  I had a limited range of motion in both ankles to start but that has since increased.  I do all of my exercises/stretches.  She has me on a 2 min run / 1 min walk program.  I did it last night and felt fine.  Just a little pain in the middle of the run, but went away very fast.  I tried to run again today (after stretching) and right away, I had a flare up.  I continued just as I used to do and it went away.  I have only run three times since April 20.  I'm beginning to think I may just have to deal with it.  Any thoughts or encouragement would be greatly appreciated.  My HIM training plan began last week and I only have two 15 min runs in.  I'm getting totally frustrated.