DOH! Col_Blitzkrieger, your stupid question is not stupid at all...I am.
I had just completed a lvl45 flashback, exited the last mission and zoomed off to the BM...I was now lvl50 again and my lvl49 power, which of course had been disabled for the flashback, was back in action as normal.
What i forgot to do was call the contact!!! I did that and got paid some inf and lo....my set bonuses were back!!
Small bug maybe? I will retest this tonight.